Computational limits to binary genes

Journal of the Royal Society Interface

Volumn 7, Issue 47, 2010, Pages 945-954

  Zabet, Nicolae Radu ^a   Chu, Dominique F ^a  

^a UNIVERSITY OF KENT   (United Kingdom)

Author keywords

Metabolic cost; Noise; Speed; Trade off

Indexed keywords

COMMERCE; COSTS; METABOLISM; OPTIMIZATION;

FIXED SPEED; HILL COEFFICIENT; LEAK-FREE; METABOLIC COST; OPTIMAL THRESHOLD; PROCESSING SPEED;

SPEED;

ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; INFORMATION PROCESSING; INFORMATION SYSTEM; MATHEMATICAL ANALYSIS; METABOLIC EQUIVALENT; NOISE; REACTION TIME;

EID: 77953170555     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2009.0474     Document Type: Article

References (28)

1. Ackers, G. K., Johnson, A. D. & Shea, M. A. 1982 Quantitative model for gene regulation by lambda phage repressor. Proc. Natl Acad. Sci. USA 79, 1129-1133. (doi:10.1073/pnas.79.4.1129)
2. Akashi, H. & Gojobori, T. 2002 Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl Acad. Sci. USA 99, 3695-3700. (doi:10.1073/pnas.062526999)
3. Arkin, A., Ross, J. & McAdams, H. H. 1998 Stochastic kinetic analysis of developmental pathway bifurcation in phage l-infected Escherichia coli cells. Genetics 149, 1633-1648. (Pubitemid 28375939)
4. Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O'Shea, E., Pilpel, Y. & Barka, N. 2006 Noise in protein expression scales with natural protein abundance. Nat. Genet. 38, 636-643. (doi:10.1038/ng1807)
5. Becskei, A., Kaufmann, B. B. & van Oudenaarden, A. 2005 Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 37, 937-944. (doi:10.1038/ng1616)
6. Bintu, L., Buchler, N. E., Garcia, H. G., Gerland, U., Hwa, T., Kondev, J. & Phillips, R. 2005 Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116-124. (doi:10.1016/j.gde.2005.02.007)
7. Bray, D. 1995 Protein molecules as computational elements in living cells. Nature 376, 307-313. (doi:10.1038/376307a0)
8. Chu, D., Zabet, N. R. & Mitavskiy, B. 2009 Models of transcription factor binding: sensitivity of activation functions to model assumptions. J. Theor. Biol. 257, 419-429. (doi:10.1016/j.jtbi.2008.11.026)
9. Dunlop, M. J., Cox III, R. S., Levine, J. H., Murray, R. M. & Elowitz, M. B. 2008 Regulatory activity revealed by dynamic correlations in gene expression noise. Nat. Genet. 40, 1493-1498. (doi:10.1038/ng.281)
10. Elf, J. & Ehrenberg, M. 2003 Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res. 13, 2475-2484. (doi:10.1101/gr.1196503) (Pubitemid 37428272)
11. Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. 2002 Stochastic gene expression in a single cell. Science 297, 1183-1186. (doi:10.1126/science.1070919)
12. Gibson, M. A. & Bruck, J. 2000 Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104, 1876-1889. (doi:10.1021/jp993732q)
13. Gillespie, D. T. 1977 Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361. (doi:10.1021/j100540a008)
14. Han, Z., Vondriska, T. M., Yang, L., MacLellan,W. R.,Weiss, J. N. & Qu, Z. 2007 Signal transduction network motifs and biological memory. J. Theor. Biol. 246, 755-761. (doi:10.1016/j.jtbi.2007.01.022)
15. Kaern, M., Elston, T. C., Blake,W. J. & Collins, J. J. 2005 Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6, 451-464. (doi:10.1038/nrg1615)
16. Kaufmann, B. B. & van Oudenaarden, A. 2007. Stochastic gene expression: from single molecules to the proteome. Curr. Opin. Genet. Dev. 17, 107-112. (doi:10.1016/j.gde.2007.02.007)
17. Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L. & Weissman, J. S. 2006 Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846. (doi:10.1038/nature04785) (Pubitemid 43910413)
18. Paulsson, J. 2004 Summing up the noise in gene networks. Nature 427, 415-418. (doi:10.1038/nature02257)
19. Paulsson, J. 2005 Models of stochastic gene expression. Phys. Life Rev. 2, 157-175. (doi:10.1016/j.plrev.2005.03.003)
20. Pedraza, J. M. & van Oudenaarden, A. 2005 Noise propagation in gene networks. Science 307, 1965-1969. (doi:10.1126/science.1109090)
21. Raj, A. & van Oudenaarden, A. 2008 Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216-226. (doi:10.1016/j.cell.2008.09.050)
22. Ramsey, S., Orrell, D. & Bolouri, H. 2005 Dizzy: stochastic simulation of large-scale genetic regulatory networks. J. Bioinformatics Comput. Biol. 3, 415-436. (doi:10.1142/S0219720005001132)
23. Rosenfeld, N., Young, J.W., Alon, U., Swain, P. S. & Elowitz, M. B. 2005 Gene regulation at the single-cell level. Science 307, 1962-1965. (doi:10.1126/science.1106914)
24. Santillan, M. & Mackey, M. C. 2004 Influence of catabolite repression and inducer exclusion on the bistable behavior of the lac operon. Biophys. J. 86, 1282-1292. (doi:10.1016/S0006-3495(04)74202-2) (Pubitemid 38295570)
25. Shibata, T. & Fujimoto, K. 2005 Noisy signal amplification in ultrasensitive signal transduction. Proc. Natl Acad. Sci. USA 102, 331-336. (doi:10.1073/pnas.0403350102)
26. Shibata, T. & Ueda, M. 2008 Noise generation, amplification and propagation in chemotactic signaling systems of living cells. BioSystems 93, 126-132. (doi:10.1016/j.biosystems.2008.04.003)
27. Spudich, J. L. & Koshland, D. E. 1976 Non-genetic individuality: chance in the single cell. Nature 262, 467-471. (doi:10.1038/262467a0)
28. van Kampen, N. G. 2007 Stochastic processes in physics and chemistry, 3rd edn. North-Holland Personal Library. Amsterdam, The Netherlands: North-Holland.