Stochasticity of metabolism and growth at the single-cell level

Nature

Volumn 514, Issue 7522, 2014, Pages 376-379

  Kiviet, Daniel J ^a,b,c   Nghe, Philippe ^a,d   Walker, Noreen ^a   Boulineau, Sarah ^a   Sunderlikova, Vanda ^a   Tans, Sander J ^a  

^a FOM INSTITUTE AMOLF   (Netherlands)

^b ETH ZURICH   (Switzerland)

^c Department of Environmental Microbiology Eawag ^*  (Switzerland)

^d CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; LAC REPRESSOR; REGULATOR PROTEIN; ESCHERICHIA COLI PROTEIN;

ENZYME ACTIVITY; FECAL COLIFORM; GENE EXPRESSION; GROWTH RATE; HETEROGENEITY; METABOLISM; MOLECULAR ANALYSIS; PROTEIN; STOCHASTICITY;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL METABOLISM; CATABOLISM; CELL EXPANSION; CELL GROWTH; CELL METABOLISM; CITRIC ACID CYCLE; CONCENTRATION (PARAMETERS); ENZYME METABOLISM; ESCHERICHIA COLI; GENE EXPRESSION; GLYCOLYSIS; GROWTH RATE; HOMEOSTASIS; NONHUMAN; PROMOTER REGION; PROTEIN EXPRESSION; REGULATORY MECHANISM; BIOLOGICAL MODEL; CELL ENLARGEMENT; CELL PROLIFERATION; ENZYMOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; LACTOSE OPERON; METABOLISM; MICROSCOPY; SINGLE CELL ANALYSIS; STATISTICS; TIME LAPSE IMAGING;

CELL ENLARGEMENT; CELL PROLIFERATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HOMEOSTASIS; LAC OPERON; MICROSCOPY; MODELS, BIOLOGICAL; SINGLE-CELL ANALYSIS; STOCHASTIC PROCESSES; TIME-LAPSE IMAGING;

EID: 84908191393     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13582     Document Type: Article

References (30)

1. Wilkinson, D. J. Stochasticmodelling for quantitative description of heterogeneous biological systems. Nature Rev. Genet. 10, 122-133 (2009).
2. Eldar, A. & Elowitz, M. B. Functional roles for noise in genetic circuits. Nature 467, 167-173 (2010).
3. Heiden, M. G. V., Cantley, L. C. & Thompson, C. B. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324, 1029-1033 (2009).
4. Lu, H. P., Xun, L. Y. & Xie, X. S. Single-molecule enzymatic dynamics. Science 282, 1877-1882 (1998).
5. Fell, D. Understanding the Control of Metabolism (Portland, 1997).
6. Herrgard, M. J., Covert, M. W. & Palsson, B. O. Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15, 70-77 (2004).
7. Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 1183-1186 (2002).
8. Ferguson, M. L. et al. Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states. Proc. Natl Acad. Sci. USA 109, 155-160 (2012).
9. Munsky, B., Neuert, G. & van Oudenaarden, A. Using gene expression noise to understand gene regulation. Science 336, 183-187 (2012).
10. Neidhardt, F. C., Ingraham, J. L. & Schaechter, M. Physiology of the Bacterial Cell: A Molecular Approach (Sinauer, 1990).
11. Rodriguez, M., Good, T. A., Wales, M. E., Hua, J. P. & Wild, J. R. Modeling allosteric regulation of de novo pyrimidine biosynthesis in Escherichia coli. J. Theor. Biol. 234, 299-310 (2005).
12. Hart, Y. et al. Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli. Mol. Cell 41, 117-127 (2011).
13. Klumpp, S., Zhang, Z. & Hwa, T. Growth rate-dependent global effects on gene expression in bacteria. Cell 139, 1366-1375 (2009).
14. Yun, H. S., Hong, J. &Lim, H. C. Regulation of ribosomesynthesis in Escherichia coli: effects of temperature and dilution rate changes. Biotechnol. Bioeng. 52, 615-624 (1996).
15. el-Mansi, E. M. & Holms, W. H. Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. J. Gen. Microbiol. 135, 2875-2883 (1989).
16. Wilson, W. A. et al. Regulation of glycogen metabolismin yeast and bacteria. FEMS Microbiol. Rev. 34, 952-985 (2010).
17. Levine, E. & Hwa, T. Stochastic fluctuations inmetabolic pathways. Proc. Natl Acad. Sci. USA 104, 9224-9229 (2007).
18. Pedraza, J. M. &van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965-1969 (2005).
19. Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B. Gene regulation at the single-cell level. Science 307, 1962-1965 (2005).
20. Dean, A. M. A molecular investigation of genotype by environment interactions. Genetics 139, 19-33 (1995).
21. Austin, D. W. et al. Gene network shaping of inherent noise spectra. Nature 439, 608-611 (2006).
22. Dunlop, M. J., Cox, R. S., III, Levine, J. H., Murray, R. M. & Elowitz, M. B. Regulatory activity revealed by dynamic correlations in gene expression noise. Nature Genet. 40, 1493-1498 (2008).
23. 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).
24. Goerke, B. & Stulke, J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nature Rev. Microbiol. 6, 613-624 (2008).
25. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64-68 (2002).
26. Walsh, K. &Koshland, D. E., Jr. Characterizationof rate-controllingsteps in vivobyuse ofanadjustable expression vector. Proc. NatlAcad. Sci. USA82, 3577-3581 (1985).
27. Wagner, A. et al. Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. Proc. Natl Acad. Sci. USA 110, 19166-19171 (2013).
28. Oh, M. K., Rohlin, L., Kao, K. C. & Liao, J. C. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277, 13175-13183 (2002).
29. Balazsi, G., van Oudenaarden, A. & Collins, J. J. Cellular decision making and biological noise: from microbes to mammals. Cell 144, 910-925 (2011).
30. Wang, Z. &Zhang, J. Impact of gene expressionnoise onorganismal fitness andthe efficacy of natural selection. Proc. Natl Acad. Sci. USA 108, E67-E76 (2011).