Deterministic and Stochastic Descriptions of Gene Expression Dynamics

Journal of Statistical Physics

Volumn 148, Issue 4, 2012, Pages 607-626

  Marathe, Rahul ^a   Bierbaum, Veronika ^a   Gomez, David ^a,b   Klumpp, Stefan ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Cell division; Genetic circuits; Growth rate; Noise; Stochastic gene expression

Indexed keywords

EID: 84866266407     PISSN: 00224715     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10955-012-0459-0     Document Type: Article

References (48)

1. Alon, U.: Biological networks: the tinkerer as an engineer. Science 301, 1866-1867 (2003).
2. Andrianantoandro, E., Basu, S., Karig, D. K., Weiss, R.: Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2, 2006. 0028 (2006).
3. Berg, O. G.: A model for the statistical fluctuations of protein numbers in a microbial population. J. Theor. Biol. 71, 587-603 (1978).
4. Berg, O. G., Paulsson, J., Ehrenberg, M.: Fluctuations in repressor control: thermodynamic constraints on stochastic focusing. Biophys. J. 79, 2944-2953 (2000).
5. Bernstein, J. A., Khodursky, A. B., Lin, P., Lin-Chao, S., Cohen, S. N.: Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99, 9697-9702 (2002).
6. Bintu, L., Buchler, N. E., Garcia, H. G., Gerland, U., Hwa, T., Kondev, J., Phillips, R.: Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116-124 (2005).
7. Bremer, H., Dennis, P. P.: Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhardt, F. C. (ed.) Escherichia coli and Salmonella, 2nd edn., pp. 1553-1569. ASM Press, Washington (1996).
8. Brenner, N., Shokef, Y.: Nonequilibrium statistical mechanics of dividing cell populations. Phys. Rev. Lett. 99, 138102 (2007).
9. Cai, L., Friedman, N., Xie, X. S.: Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358-362 (2006).
10. Cook, D. L., Gerber, A. N., Tapscott, S. J.: Modeling stochastic gene expression: implications for haploinsufficiency. Proc. Natl. Acad. Sci. USA 95, 15641-15646 (1998).
11. Cookson, N. A., Cookson, S. W., Tsimring, L. S., Hasty, J.: Cell cycle-dependent variations in protein concentration. Nucleic Acids Res. 38, 2676-2681 (2010).
12. Cooper, S., Helmstetter, C. E.: Chromosome replication and the division cycle of Escherichia coli B/r. J. Mol. Biol. 31, 519-540 (1968).
13. Cooper, S.: Distinguishing between linear and exponential cell growth during the division cycle: single-cell studies, cell-culture studies, and the object of cell-cycle research. Theor. Biol. Med. Model. 3, 10 (2006).
14. Csete, M. E., Doyle, J. C.: Reverse engineering of biological complexity. Science 295, 1664-1669 (2002).
15. Elowitz, M. B., Levine, A. J., Siggia, E. D., Swain, P. S.: Stochastic gene expression in a single cell. Science 297, 1183-1186 (2002).
16. Golding, I., Paulsson, J., Zawilski, S. M., Cox, E. C.: Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025-1036 (2005).
17. Guido, N. J., Wang, X., Adalsteinsson, D., McMillen, D., Hasty, J., Cantor, C. R., Elston, T. C., Collins, J. J.: A bottom-up approach to gene regulation. Nature 439, 856-860 (2006).
18. Guptasarma, P.: Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? BioEssays 17, 987-997 (1995).
19. Hasty, J., Pradines, J., Dolnik, M., Collins, J. J.: Noise-based switches and amplifiers for gene expression. Proc. Natl. Acad. Sci. USA 97, 2075-2080 (2000).
20. Hasty, J., McMillen, D., Collins, J. J.: Engineered gene circuits. Nature 420, 224-230 (2002).
21. Kaern, M., Elston, T. C., Blake, W. J., Collins, J. J.: Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6, 451-464 (2005).
22. Klumpp, S., Hwa, T.: Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc. Natl. Acad. Sci. USA 105, 20245-20250 (2008).
23. Klumpp, S., Hwa, T.: Stochasticity and traffic jams in the transcription of ribosomal RNA: intriguing role of termination and antitermination. Proc. Natl. Acad. Sci. USA 105, 18159-18164 (2008).
24. Klumpp, S., Zhang, Z., Hwa, T.: Growth rate-dependent global effects on gene expression in bacteria. Cell 139, 1366-1375 (2009).
25. Klumpp, S.: Pausing and backtracking in transcription under dense traffic conditions. J. Stat. Phys. 142, 1252-1267 (2011).
26. Klumpp, S.: Growth-rate dependence reveals design principles of plasmid copy number control. PLoS ONE 6, e20403 (2011).
27. Ko, M. S.: A stochastic model for gene induction. J. Theor. Biol. 153, 181-194 (1991).
28. Kwok, R.: Five hard truths for synthetic biology. Nature 463, 288-290 (2010).
29. McAdams, H. H., Arkin, A.: Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA 94, 814-819 (1997).
30. Mitarai, N., Dodd, I. B., Crooks, M. T., Sneppen, K.: The generation of promoter-mediated transcriptional noise in bacteria. PLoS Comput. Biol. 4, e1000109 (2008).
31. Nath, K., Koch, A. L.: Protein degradation in Escherichia coli. I. Measurement of rapidly and slowly decaying components. J. Biol. Chem. 245, 2889-2900 (1970).
32. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., van Oudenaarden, A.: Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69-73 (2002).
33. Paulsson, J.: Summing up the noise in gene networks. Nature 427, 415-418 (2004).
34. Paulsson, J.: Models of stochastic gene expression. Phys. Life Rev. 2, 157-175 (2005).
35. Peccoud, J., Ycart, B.: Markovian modeling of gene-product synthesis. Theor. Popul. Biol. 48, 222-234 (1995).
36. Rao, C. V., Wolf, D. M., Arkin, A. P.: Control, exploitation and tolerance of intracellular noise. Nature 420, 231-237 (2002).
37. Reeh, S., Pedersen, S.: Post-translational modification of Escherichia coli ribosomal protein S6. Mol. Gen. Genet. 173, 183-187 (1979).
38. Scott, M., Hwa, T., Ingalls, B.: Deterministic characterization of stochastic genetic circuits. Proc. Natl. Acad. Sci. USA 104, 7402-7407 (2007).
39. Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z., Hwa, T.: Interdependence of cell growth and gene expression: origins and consequences. Science 330, 1099-1102 (2010).
40. Spudich, J. L., Koshland, D. E. Jr.: Non-genetic individuality: chance in the single cell. Nature 262, 467-471 (1976).
41. Swain, P. S., Elowitz, M. B., Siggia, E. D.: Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 99, 12795-12800 (2002).
42. Tan, C., Marguet, P., You, L.: Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 5, 842-848 (2009).
43. Taniguchi, Y., Choi, P. J., Li, G. W., Chen, H., Babu, M., Hearn, J., Emili, A., Xie, X. S.: Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329, 533-538 (2010).
44. Thattai, M., van Oudenaarden, A.: Intrinsic noise in gene regulatory networks. Proc. Natl. Acad. Sci. USA 98, 8614-8619 (2001).
45. Walczak, A. M., Sasai, M., Wolynes, P. G.: Self-consistent proteomic field theory of stochastic gene switches. Biophys. J. 88, 828-850 (2005).
46. Wall, M. E., Hlavacek, W. S., Savageau, M. A.: Design of gene circuits: lessons from bacteria. Nat. Rev. Genet. 5, 34-42 (2004).
47. Wang, P., Robert, L., Pelletier, J., Dang, W. L., Taddei, F., Wright, A., Jun, S.: Robust growth of Escherichia coli. Curr. Biol. 20, 1099-1103 (2010).
48. Yu, J., Xiao, J., Ren, X., Lao, K., Xie, X. S.: Probing gene expression in live cells, one protein molecule at a time. Science 311, 1600-1603 (2006).