Cosentino Lagomarsino, M., Jona, P., Bassetti, B. & Isambert, H. Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc. Natl Acad. Sci. USA104, 5516–5520 (2007). ArticleCASPubMedPubMed Central Google Scholar
Balázsi, G., Heath, A. P., Shi, L. & Gennaro, M. L. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol.4, 225 (2008). ArticlePubMedPubMed Central Google Scholar
Wall, M. E., Hlavacek, W. S. & Savageau, M. A. Design of gene circuits: lessons from bacteria. Nature Rev. Genet.5, 34–42 (2004). ArticleCASPubMed Google Scholar
Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman and Hall/CRC, 2006). Google Scholar
Mangan, S. & Alon, U. Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA100, 11980–11985 (2003). ArticleCASPubMedPubMed Central Google Scholar
Prill, R. J., Iglesias, P. A. & Levchenko, A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol.3, e343 (2005). ArticleCASPubMedPubMed Central Google Scholar
Wall, M. E., Dunlop, M. J. & Hlavacek, W. S. Multiple functions of a feed-forward-loop gene circuit. J. Mol. Biol.349, 501–514 (2005). ArticleCASPubMed Google Scholar
Stock, A. M., Robinson, V. L. & Goudreau, P. N. Two-component signal transduction. Annu. Rev. Biochem.69, 183–215 (2000). ArticleCASPubMed Google Scholar
Martínez-Antonio, A., Janga, S. C. & Thieffry, D. Functional organisation of Escherichia coli transcriptional regulatory network. J. Mol. Biol.381, 238–247 (2008). ArticleCASPubMedPubMed Central Google Scholar
Ray, J. C. J. & Igoshin, O. A. Adaptable functionality of transcriptional feedback in bacterial two-component systems. PLoS Comput. Biol.6, e1000676 (2010). ArticleCASPubMedPubMed Central Google Scholar
Shin, D., Lee, E.-J., Huang, H. & Groisman, E. A positive feedback loop promotes transcription surge that jump-starts Salmonella virulence circuit. Science314, 1607–1609 (2006). This study demonstrates the physiological importance of network dynamics for a virulent microorganism. ArticleCASPubMed Google Scholar
Savageau, M. A. Design principles for elementary gene circuits: elements, methods, and examples. Chaos11, 142–159 (2001). ArticleCASPubMed Google Scholar
Chen, W. W., Niepel, M. & Sorger, P. K. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev.24, 1861–1875 (2010). ArticleCASPubMedPubMed Central Google Scholar
Hlavacek, W. S. & Savageau, M. A. Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. J. Mol. Biol.248, 739–755 (1995). ArticleCASPubMed Google Scholar
Perutz, M. F. Mechanisms of cooperativity and allosteric regulation in proteins. Q. Rev. Biophys.22, 139–237 (1989). ArticleCASPubMed Google Scholar
Goldbeter, A. & Koshland, D. E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl Acad. Sci. USA78, 6840–6844 (1981). ArticleCASPubMedPubMed Central Google Scholar
Kim, S. Y. & Ferrell, J. E. Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell128, 1133–1145 (2007). ArticleCASPubMed Google Scholar
Palani, S. & Sarkar, C. A. Positive receptor feedback during lineage commitment can generate ultrasensitivity to ligand and confer robustness to a bistable switch. Biophys. J.95, 1575–1589 (2008). ArticleCASPubMedPubMed Central Google Scholar
Wang, L. et al. Bistable switches control memory and plasticity in cellular differentiation. Proc. Natl Acad. Sci. USA106, 6638–6643 (2009). ArticleCASPubMedPubMed Central Google Scholar
Cluzel, P., Surette, M. & Leibler, S. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science287, 1652–1655 (2000). ArticleCASPubMed Google Scholar
LaPorte, D. C. & Koshland, D. E. Phosphorylation of isocitrate dehydrogenase as a demonstration of enhanced sensitivity in covalent regulation. Nature305, 286–290 (1983). ArticleCASPubMed Google Scholar
Buchler, N. E., Gerland, U. & Hwa, T. Nonlinear protein degradation and the function of genetic circuits. Proc. Natl Acad. Sci. USA102, 9559–9564 (2005). ArticleCASPubMedPubMed Central Google Scholar
Buchler, N. E. & Louis, M. Molecular titration and ultrasensitivity in regulatory networks. J. Mol. Biol.384, 1106–1119 (2008). ArticleCASPubMed Google Scholar
Tiwari, A., Balázsi, G., Gennaro, M. L. & Igoshin, O. A. The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Phys. Biol.7, 036005 (2010). ArticleCASPubMedPubMed Central Google Scholar
Legewie, S., Dienst, D., Wilde, A., Herzel, H. & Axmann, I. M. Small RNAs establish delays and temporal thresholds in gene expression. Biophys. J.95, 3232–3238 (2008). ArticleCASPubMedPubMed Central Google Scholar
Xiong, W. & Ferrell, J. E. A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature426, 460–465 (2003). ArticleCASPubMed Google Scholar
Berg, O. G., Paulsson, J. & Ehrenberg, M. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J.79, 1228–1236 (2000). ArticleCASPubMedPubMed Central Google Scholar
Igoshin, O. A., Price, C. W. & Savageau, M. A. Signalling network with a bistable hysteretic switch controls developmental activation of the F transcription factor in Bacillus subtilis. Mol. Microbiol.61, 165–184 (2006). ArticleCASPubMed Google Scholar
Igoshin, O. A., Brody, M. S., Price, C. W. & Savageau, M. A. Distinctive topologies of partner-switching signaling networks correlate with their physiological roles. J. Mol. Biol.369, 1333–1352 (2007). ArticleCASPubMedPubMed Central Google Scholar
Craciun, G., Tang, Y. & Feinberg, M. Understanding bistability in complex enzyme-driven reaction networks. Proc. Natl Acad. Sci. USA103, 8697–8702 (2006). ArticleCASPubMedPubMed Central Google Scholar
Thomas, R. & Kaufman, M. Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos11, 170–179 (2001). ArticlePubMed Google Scholar
Klumpp, S., Zhang, Z. & Hwa, T. Growth rate-dependent global effects on gene expression in bacteria. Cell139, 1366–1375 (2009). A re-evaluation of classic microbiology data combined with new theory reveals that the growth rate has widespread consequences for bacterial phenotypes. ArticlePubMedPubMed Central Google Scholar
Tan, C., Marguet, P. & You, L. Emergent bistability by a growth-modulating positive feedback circuit. Nature Chem. Biol.5, 842–848 (2009). An elegant experimental approach that demonstrates growth-modulated bistability. ArticleCAS Google Scholar
Gottesman, S. Proteolysis in bacterial regulatory circuits. Annu. Rev. Cell Dev. Biol.19, 565–587 (2003). ArticleCASPubMed Google Scholar
Rotem, E. et al. Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc. Natl Acad. Sci. USA107, 12541–12546 (2010). ArticleCASPubMedPubMed Central Google Scholar
Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science305, 1622–1625 (2004). ArticleCASPubMed Google Scholar
Reed, M. C., Lieb, A. & Nijhout, F. F. The biological significance of substrate inhibition: a mechanism with diverse functions. Bioessays32, 422–429 (2010). ArticleCASPubMed Google Scholar
Chaudhury, S. & Igoshin, O. A. Dynamic disorder-driven substrate inhibition and bistability in a simple enzymatic reaction. J. Phys. Chem. B113, 13421–13428 (2009). ArticleCASPubMed Google Scholar
Igoshin, O. A., Alves, R. & Savageau, M. A. Hysteretic and graded responses in bacterial two-component signal transduction. Mol. Microbiol.68, 1196–1215 (2008). ArticleCASPubMedPubMed Central Google Scholar
Ishii, N. et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science316, 593–597 (2007). ArticleCASPubMed Google Scholar
Lynch, M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl Acad. Sci. USA104, 8597–8604 (2007). ArticleCASPubMedPubMed Central Google Scholar
Rice, S. Evolutionary Theory (Sinauer Associates, Inc., 2004). Google Scholar
Miyashiro, T. & Goulian, M. High stimulus unmasks positive feedback in an autoregulated bacterial signaling circuit. Proc. Natl Acad. Sci. USA105, 17457–17462 (2008). ArticleCASPubMedPubMed Central Google Scholar
Angeli, D., Ferrell, J. E. & Sontag, E. D. Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl Acad. Sci. USA101, 1822–1827 (2004). ArticleCASPubMedPubMed Central Google Scholar
Eguchi, Y., Ishii, E., Hata, K. & Utsumi, R. Regulation of acid resistance by connectors of two-component signal transduction systems in Escherichia coli. J. Bacteriol.193, 1222–1228 (2011). ArticleCASPubMed Google Scholar
Burton, N. A., Johnson, M. D., Antczak, P., Robinson, A. & Lund, P. A. Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics. J. Mol. Biol.401, 726–742 (2010). These authors take a detail-oriented experimental approach to evaluating the dynamics of gene-regulatory networks without losing sight of the 'big picture'. ArticleCASPubMed Google Scholar
Savageau, M. A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature252, 546–549 (1974). ArticleCASPubMed Google Scholar
Traxler, M. F. et al. Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Mol. Microbiol.79, 830–845 (2010). ArticleCASPubMedPubMed Central Google Scholar
Hoffer, S. M., Westerhoff, H. V., Hellingwerf, K. J., Postma, P. W. & Tommassen, J. Autoamplification of a two-component regulatory system results in “learning” behavior. J. Bacteriol.183, 4914–4917 (2001). ArticleCASPubMedPubMed Central Google Scholar
Chastanet, A. et al. Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proc. Natl Acad. Sci. USA107, 8486–8491 (2010). ArticleCASPubMedPubMed Central Google Scholar
Bischofs, I. B., Hug, J. A., Liu, A. W., Wolf, D. M. & Arkin, A. P. Complexity in bacterial cell–cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay. Proc. Natl Acad. Sci. USA106, 6459–6464 (2009). ArticleCASPubMedPubMed Central Google Scholar
Schultz, D., Wolynes, P. G., Jacob, E. & Onuchic, J. N. Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc. Natl Acad. Sci. USA106, 21027–21034 (2009). ArticleCASPubMedPubMed Central Google Scholar
Saini, S., Ellermeier, J. R., Slauch, J. M. & Rao, C. V. The role of coupled positive feedback in the expression of the SPI1 type three secretion system in Salmonella. PLoS Pathog.6, e1001025 (2010). ArticleCASPubMedPubMed Central Google Scholar
Nguyen, L. K. & Kulasiri, D. On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems. BMC Syst. Biol.3, 51 (2009). ArticleCASPubMedPubMed Central Google Scholar
Stekel, D. J. & Jenkins, D. J. Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression. BMC Syst. Biol.2, 6 (2008). ArticleCASPubMedPubMed Central Google Scholar
Bhartiya, S., Chaudhary, N., Venkatesh, K. V. & Doyle, F. J. Multiple feedback loop design in the tryptophan regulatory network of Escherichia coli suggests a paradigm for robust regulation of processes in series. J. R. Soc. Interface3, 383–391 (2006). ArticleCASPubMed Google Scholar
Curtis, P. D. & Brun, Y. V. Getting in the loop: regulation of development in Caulobacter crescentus. Microbiol. Mol. Biol. Rev.74, 13–41 (2010). ArticleCASPubMedPubMed Central Google Scholar
Jenal, U. The role of proteolysis in the Caulobacter crescentus cell cycle and development. Res. Microbiol.160, 687–695 (2009). ArticleCASPubMed Google Scholar
Thanbichler, M. & Shapiro, L. Chromosome organization and segregation in bacteria. J. Struct. Biol.156, 292–303 (2006). ArticleCASPubMed Google Scholar
Biondi, E. G. et al. Regulation of the bacterial cell cycle by an integrated genetic circuit. Nature444, 899–904 (2006). ArticleCASPubMed Google Scholar
Paul, R. et al. Allosteric regulation of histidine kinases by their cognate response regulator determines cell fate. Cell133, 452–461 (2008). ArticleCASPubMedPubMed Central Google Scholar
Chen, Y. E. et al. Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium. Proc. Natl Acad. Sci. USA108, 1052–1057 (2011). An experimentally driven study of theC. crescentuscell cycle, making use of mathematical modelling and simulation to circumvent experimental constraints and arrive at a compelling conceptual model. ArticleCASPubMed Google Scholar
Hallez, R., Bellefontaine, A.-F., Letesson, J.-J. & De Bolle, X. Morphological and functional asymmetry in α-proteobacteria. Trends Microbiol.12, 361–365 (2004). ArticleCASPubMed Google Scholar
Ackermann, M., Stearns, S. C. & Jenal, U. Senescence in a bacterium with asymmetric division. Science300, 1920 (2003). ArticleCASPubMed Google Scholar
Stewart, E. J., Madden, R., Paul, G. & Taddei, F. Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol.3, e45 (2005). ArticleCASPubMedPubMed Central Google Scholar
Sprinzak, D. & Elowitz, M. B. Reconstruction of genetic circuits. Nature438, 443–448 (2005). ArticleCASPubMed Google Scholar
Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature403, 339–342 (2000). ArticleCASPubMed Google Scholar
Weiss, R. Cellular Computation and Communications Using Engineered Genetic Regulatory Networks. Thesis, Massachussets Institute of Technology (2001). Google Scholar
Atkinson, M. R., Savageau, M. A., Myers, J. T. & Ninfa, A. J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell113, 597–607 (2003). ArticleCASPubMed Google Scholar
Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature403, 335–338 (2000). ArticleCASPubMed Google Scholar
Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. Real-time kinetics of gene activity in individual bacteria. Cell123, 1025–1036 (2005). ArticleCASPubMed Google Scholar
Pedraza, J. M. & Paulsson, J. Effects of molecular memory and bursting on fluctuations in gene expression. Science319, 339–343 (2008). ArticleCASPubMed Google Scholar
Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B. Gene regulation at the single-cell level. Science307, 1962–1965 (2005). ArticleCASPubMed Google Scholar
Pedraza, J. M. & van Oudenaarden, A. Noise propagation in gene networks. Science307, 1965–1969 (2005). ArticleCASPubMed Google Scholar
Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science297, 1183–1186 (2002). ArticleCASPubMed Google Scholar
Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol.355, 619–627 (2006). ArticleCASPubMed Google Scholar
Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl Acad. Sci. USA101, 6355–6360 (2004). ArticleCASPubMedPubMed Central Google Scholar
Salis, H. M., Mirsky, E. A. & Voigt, C. A. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotech.27, 946–950 (2009). ArticleCAS Google Scholar
Na, D., Lee, S. & Lee, D. Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst. Biol.4, 71 (2010). ArticleCASPubMedPubMed Central Google Scholar
Miyazaki, K. Creating random mutagenesis libraries by megaprimer PCR of whole plasmid (MEGAWHOP). Methods Mol. Biol.231, 23–28 (2003). CASPubMed Google Scholar
Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature456, 516–519 (2008). This article describes the engineering of a robust, tunable synthetic oscillator. The results illustrate the importance of post-transcriptional delays for the dynamic functionality of gene-regulatory networks. ArticleCASPubMedPubMed Central Google Scholar
Lim, W. A. Designing customized cell signalling circuits. Nature Rev. Mol. Cell Biol.11, 393–403 (2010). ArticleCAS Google Scholar
Martin, V. J. J., Pitera, D. J., Withers, S. T., Newman, J. D. & Keasling, J. D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nature Biotech.21, 796–802 (2003). ArticleCAS Google Scholar
Dueber, J. E. et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nature Biotech.27, 753–759 (2009). A clever non-transcriptional-modification scheme is shown to greatly boost efficiency in a synthetic metabolic pathway, laying fundamental groundwork for mechanistic synthetic biology. ArticleCAS Google Scholar
Marles-Wright, J. & Lewis, R. J. The stressosome: molecular architecture of a signalling hub. Biochem. Soc. Trans.38, 928–933 (2010). ArticleCASPubMed Google Scholar
Marles-Wright, J. et al. Molecular architecture of the “stressosome,” a signal integration and transduction hub. Science322, 92–96 (2008). ArticleCASPubMed Google Scholar
Saiz, L. & Vilar, J. M. J. Ab initio thermodynamic modeling of distal multisite transcription regulation. Nucleic Acids Res.36, 726–731 (2008). ArticleCASPubMed Google Scholar
Long, T. et al. Quantifying the integration of quorum-sensing signals with single-cell resolution. PLoS Biol.7, e1000068 (2009). ArticleCASPubMed Central Google Scholar
Feinberg, M. The existence and uniqueness of steady states for a class of chemical reaction networks. Arch. Rational Mech. Anal.132, 311–370 (1995). Article Google Scholar
Shinar, G. & Feinberg, M. Structural sources of robustness in biochemical reaction networks. Science327, 1389–1391 (2010). ArticleCASPubMed Google Scholar
Batchelor, E. & Goulian, M. Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system. Proc. Natl Acad. Sci. USA100, 691–696 (2003). ArticleCASPubMedPubMed Central Google Scholar
Shinar, G., Milo, R., Martínez, M. R. & Alon, U. Input output robustness in simple bacterial signaling systems. Proc. Natl Acad. Sci. USA104, 19931–19935 (2007). ArticleCASPubMedPubMed Central Google Scholar