A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell
Open accessAbstract
By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Genetic regulatory mechanisms in the synthesis of proteins.
Jacob, F., & Monod, J. (1961) · Journal of Molecular Biology · doi:10.1016/s0022-2836(61)80072-7 · Cited by 5,995 · see citing works
Stochasticity in gene expression: from theories to phenotypes
Kærn, M., Elston, T. C., Blake, W. J., & Collins, J. J. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1615 · Cited by 2,271 · see citing works
Arkin, A. P., Ross, J., & McAdams, H. H. (1998) · Genetics · doi:10.1093/genetics/149.4.1633 · Cited by 1,492 · see citing works
Stochastic protein expression in individual cells at the single molecule level
Cai, L., Friedman, N., & Xie, X. S. (2006) · Nature · doi:10.1038/nature04599 · Cited by 1,145 · see citing works
Self-citationGene Regulation at the Single-Cell Level
Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., & Elowitz, M. B. (2005) · Science · doi:10.1126/science.1106914 · Cited by 1,104 · see citing works
Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
Elf, J., Li, G., & Xie, X. (2007) · Science · doi:10.1126/science.1141967 · Cited by 1,063 · see citing works
Self-citationMultistability in the lactose utilization network of Escherichia coli
Ozbudak, E. M., Thattai, M., Lim, H. N., Shraiman, B. I., & van Oudenaarden, A. (2004) · Nature · doi:10.1038/nature02298 · Cited by 1,030 · see citing works
Probing Gene Expression in Live Cells, One Protein Molecule at a Time
Yu, J., Xiao, J., Ren, X., Lao, K., & Xie, X. S. (2006) · Science · doi:10.1126/science.1119623 · Cited by 918 · see citing works
Self-citationENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON
Novick, A., & Weiner, M. (1957) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.43.7.553 · Cited by 891 · see citing works
Optimality and evolutionary tuning of the expression level of a protein
Dekel, E., & Alon, U. (2005) · Nature · doi:10.1038/nature03842 · Cited by 766 · see citing works
Dubnau, D. A., & Losick, R. M. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05249.x · Cited by 729 · see citing works
Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression
Friedman, N., Cai, L., & Xie, X. S. (2006) · Physical Review Letters · doi:10.1103/physrevlett.97.168302 · Cited by 700 · see citing works
Self-citationISOLATION OF THE LAC REPRESSOR
Gilbert, W., & Müller‐Hill, B. (1966) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.56.6.1891 · Cited by 657 · see citing works
A Genetic Switch, Phage Lambda Revisited
Ptashne, M. (2004) · Cited by 488 · see citing works
The three operators of the lac operon cooperate in repression.
Oehler, S., Eismann, E. R., Krämer, H., & Müller‐Hill, B. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb08199.x · Cited by 473 · see citing works
lac repressor forms loops with linear DNA carrying two suitably spaced lac operators.
Krämer, H., Niemöller, M., Amouyal, M., Révet, B., von Wilcken‐Bergmann, B., & Müller‐Hill, B. (1987) · The EMBO Journal · doi:10.1002/j.1460-2075.1987.tb02390.x · Cited by 351 · see citing works
Single-Molecule Approach to Molecular Biology in Living Bacterial Cells
Xie, X. S., Choi, P. J., Li, G., Lee, N. K., & Lia, G. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092607.174640 · Cited by 348 · see citing works
Self-citationTranscription and translation initiation frequencies of the Escherichia coli lac operon
Kennell, D. E., & Riezman, H. (1977) · Journal of Molecular Biology · doi:10.1016/0022-2836(77)90279-0 · Cited by 323 · see citing works
Müller‐Hill, B. (1996) · De Gruyter eBooks · doi:10.1515/9783110879476 · Cited by 320 · see citing works
Cohen, G. N., & Monod, J. (1957) · Bacteriological Reviews · doi:10.1128/br.21.3.169-194.1957 · Cited by 268 · see citing works
Self-regulating gene: An exact solution
Hornos, J. E. M., Schultz, D., Innocentini, G. C. P., Wang, J., Walczak, A. M., Onuchic, J. N., & Wolynes, P. G. (2005) · Physical Review E · doi:10.1103/physreve.72.051907 · Cited by 263 · see citing works
Vilar, J. M. G., Guet, C. C., & Leibler, S. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200301125 · Cited by 200 · see citing works
Interaction of effecting ligands with lac repressor and repressor-operator complex
Barkley, M. D., Riggs, A. D., Jobe, A. H., & Bourgeois, S. (1975) · Biochemistry · doi:10.1021/bi00679a024 · Cited by 179 · see citing works
Revzin, A., & von Hippel, P. H. (1977) · Biochemistry · doi:10.1021/bi00641a002 · Cited by 162 · see citing works
Predicting stochastic gene expression dynamics in single cells
Mettetal, J. T., Muzzey, D., Pedraza, J. M., Özbudak, E. M., & van Oudenaarden, A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509874103 · Cited by 162 · see citing works
Artyomov, M. N., Das, J., Kardar, M., & Chakraborty, A. K. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706110104 · Cited by 110 · see citing works
Kinetic studies of inducer binding to lac repressor.operator complex.
Dunaway, M., Olson, J. S., Rosenberg, J. M., Kallai, O. B., Dickerson, R. E., & Matthews, K. S. (1980) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)70435-9 · Cited by 40 · see citing works
Flagged first, then by citations
1 of the 28 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- [6]Monod J Jacob F J. Mol. Biol 1961 3 318 356 13718526
- [25]Rezvin A von Hippel PH Biochem 1977 16 4769 4776 20938
Cited by
Sorted by citations
Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., & Xie, X. S. (2010) · Science · doi:10.1126/science.1188308 · Cited by 1,982 · see citing works
Self-citationFunctional roles for noise in genetic circuits
Eldar, A., & Elowitz, M. B. (2010) · Nature · doi:10.1038/nature09326 · Cited by 1,440 · see citing works
Carbon Nanomaterials in Biosensors: Should You Use Nanotubes or Graphene?
Yang, W. R., Ratinac, K. R., Ringer, S. P., Thordarson, P., Gooding, J. J., & Braet, F. (2010) · Angewandte Chemie International Edition · doi:10.1002/anie.200903463 · Cited by 1,432 · see citing works
Systematic characterization of maturation time of fluorescent proteins in living cells
Balleza, E., Kim, J. M., & Cluzel, P. (2017) · Nature Methods · doi:10.1038/nmeth.4509 · Cited by 486 · see citing works
Genetic Determinants and Cellular Constraints in Noisy Gene Expression
Sánchez, Á., & Golding, I. (2013) · Science · doi:10.1126/science.1242975 · Cited by 460 · see citing works
Mechanism of Transcriptional Bursting in Bacteria
Chong, S., Chen, C., Ge, H., & Xie, X. S. (2014) · Cell · doi:10.1016/j.cell.2014.05.038 · Cited by 428 · see citing works
Self-citationCentral dogma at the single-molecule level in living cells
Li, G., & Xie, X. S. (2011) · Nature · doi:10.1038/nature10315 · Cited by 442 · see citing works
Self-citationStructural advances for the major facilitator superfamily (MFS) transporters
Yan, N. (2013) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2013.01.003 · Cited by 418 · see citing works
General properties of transcriptional time series in Escherichia coli
So, L., Ghosh, A., Zong, C. C., Sepúlveda, L. A., Segev, R., & Golding, I. (2011) · Nature Genetics · doi:10.1038/ng.821 · Cited by 384 · see citing works
Yaginuma, H., Kawai, S., Tabata, K. V., Tomiyama, K., Kakizuka, A., Komatsuzaki, T., Noji, H., & Imamura, H. (2014) · Scientific Reports · doi:10.1038/srep06522 · Cited by 387 · see citing works
Development and applications of single-cell transcriptome analysis
Tang, F., Lao, K., & Surani, M. A. (2011) · Nature Methods · doi:10.1038/nmeth.1557 · Cited by 337 · see citing works
Ma, P., Amemiya, H. M., He, L. L., Gandhi, S. J., Nicol, R., Bhattacharyya, R. P., Smillie, C. S., & Hung, D. T. (2023) · Cell · doi:10.1016/j.cell.2023.01.002 · Cited by 291 · see citing works
The role of physiological heterogeneity in microbial population behavior
Lidstrom, M. E., & Konopka, M. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.436 · Cited by 295 · see citing works
Classic and contemporary approaches to modeling biochemical reactionsPreprint
Chen, W. W., Niepel, M., & Sorger, P. K. (2010) · Genes & Development · doi:10.1101/gad.1945410 · Cited by 287 · see citing works
Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals
Wan, X., Volpetti, F., Petrova, E., French, C. E., Maerkl, S. J., & Wang, B. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0244-3 · Cited by 283 · see citing works
Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection
Zeng, L., Skinner, S. O., Zong, C. C., Sippy, J., Feiss, M. G., & Golding, I. (2010) · Cell · doi:10.1016/j.cell.2010.03.034 · Cited by 272 · see citing works
Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells
Singer, Z. S., Yong, J., Tischler, J., Hackett, J. A., Altınok, A., Surani, M. A., Cai, L., & Elowitz, M. B. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.029 · Cited by 275 · see citing works
Self-citationExploring bacterial cell biology with single-molecule tracking and super-resolution imaging
Gahlmann, A., & Moerner, W. E. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3154 · Cited by 260 · see citing works
Memory and Fitness Optimization of Bacteria under Fluctuating Environments
Lambert, G., & Kussell, E. L. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004556 · Cited by 248 · see citing works
The transcription unit architecture of the Escherichia coli genome
Cho, B., Zengler, K., Qiu, Y. L., Park, Y. S., Knight, E. M., Barrett, C. L., Gao, Y., & Palsson, B. Ø. (2009) · Nature Biotechnology · doi:10.1038/nbt.1582 · Cited by 253 · see citing works
Phenotypic bistability in Escherichia coli's central carbon metabolism
Kotte, O., Volkmer, B., Radzikowski, J. L., & Heinemann, M. (2014) · Molecular Systems Biology · doi:10.15252/msb.20135022 · Cited by 242 · see citing works
Bothma, J. P., García, H. G., Esposito, E., Schlissel, G., Gregor, T., & Levine, M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1410022111 · Cited by 245 · see citing works
Shining Light on the Microbial World
Huang, W. E., Li, M., Jarvis, R. M., Goodacre, R., & Banwart, S. A. (2010) · Advances in applied microbiology · doi:10.1016/s0065-2164(10)70005-8 · Cited by 224 · see citing works
The phenomenon of microbial uncultivability
Epstein, S. (2013) · Current Opinion in Microbiology · doi:10.1016/j.mib.2013.08.003 · Cited by 225 · see citing works
Regulation of Noise in Gene Expression
Sánchez, Á., Choubey, S., & Kondev, J. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130401 · Cited by 194 · see citing works
Jun, Y., Sheikholeslami, S. N., Hostetter, D. R., Tajon, C. A., Craik, C. S., & Alivisatos, A. P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907367106 · Cited by 189 · see citing works
What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism
Symmons, O., & Raj, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.023 · Cited by 180 · see citing works
Transcription Dynamics in Living Cells
Lenstra, T. L., Rodriguez, J., Chen, H., & Larson, D. R. (2016) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010838 · Cited by 179 · see citing works
Random sequences rapidly evolve into de novo promoters
Yona, A. H., Alm, E. J., & Gore, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04026-w · Cited by 182 · see citing works
Stochastic Switching of Cell Fate in Microbes
Norman, T. M., Lord, N. D., Paulsson, J., & Losick, R. M. (2015) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091213-112852 · Cited by 164 · see citing works
Phenotypic switching in gene regulatory networks
Thomas, P., Popović, N., & Grima, R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400049111 · Cited by 172 · see citing works
Allostery in the LacI/GalR family: variations on a theme
Swint‐Kruse, L., & Matthews, K. S. (2009) · Current Opinion in Microbiology · doi:10.1016/j.mib.2009.01.009 · Cited by 172 · see citing works
WKB theory of large deviations in stochastic populations
Assaf, M., & Meerson, B. (2017) · Journal of Physics A Mathematical and Theoretical · doi:10.1088/1751-8121/aa669a · Cited by 166 · see citing works
Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics
Iversen, L., Tu, H.-L., Lin, W.-C., Christensen, S. M., Abel, S. M., Iwig, J., Wu, H.-J., Gureasko, J., Rhodes, C., Petit, R. S., et al. (2014) · Science · doi:10.1126/science.1250373 · Cited by 154 · see citing works
Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression
Maheshri, N., Zopf, C. J., Quinn, K., & Zeidman, J. (2013) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 164 · see citing works
Analytical techniques for single-cell metabolomics: state of the art and trends
Amantonico, A., Urban, P. L., & Zenobi, R. (2010) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-010-3850-1 · Cited by 157 · see citing works
The potential of microfluidic water-in-oil droplets in experimental biology
Schaerli, Y., & Hollfelder, F. (2009) · Molecular BioSystems · doi:10.1039/b907578j · Cited by 149 · see citing works
Opposing effects of target overexpression reveal drug mechanisms
Palmer, A. C., & Kishony, R. (2014) · Nature Communications · doi:10.1038/ncomms5296 · Cited by 139 · see citing works
Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression
Sánchez, Á., García, H. G., Jones, D., Phillips, R., & Kondev, J. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001100 · Cited by 144 · see citing works
Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation
Uphoff, S., Lord, N. D., Okumuş, B., Potvin-Trottier, L., Sherratt, D. J., & Paulsson, J. (2016) · Science · doi:10.1126/science.aac9786 · Cited by 148 · see citing works
Perspectives on the contribution of lactic acid bacteria to cheese flavor development
Steele, J. L., Broadbent, J. R., & Kok, J. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.12.001 · Cited by 143 · see citing works
Integrated microfluidic systems for high-performance genetic analysis
Liu, P., & Mathies, R. A. (2009) · Trends in biotechnology · doi:10.1016/j.tibtech.2009.07.002 · Cited by 142 · see citing works
Quantitative dissection of the simple repression input–output function
García, H. G., & Phillips, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1015616108 · Cited by 127 · see citing works
Capitanio, M., Canepari, M., Maffei, M., Beneventi, D., Mónico, C., Vanzi, F., Bottinelli, R., & Pavone, F. S. (2012) · Nature Methods · doi:10.1038/nmeth.2152 · Cited by 139 · see citing works
Hammar, P., Walldén, M., Fange, D., Persson, F., Baltekin, Ö., Ullman, G., Leroy, P., & Elf, J. (2014) · Nature Genetics · doi:10.1038/ng.2905 · Cited by 126 · see citing works
Galactose metabolic genes in yeast respond to a ratio of galactose and glucose
Escalante-Chong, R., Savir, Y., Carroll, S. M., Ingraham, J., Wang, J., Marx, C. J., & Springer, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418058112 · Cited by 132 · see citing works
Determining the Stability of Genetic Switches: Explicitly Accounting for mRNA Noise
Assaf, M., Roberts, E., & Luthey-Schulten, Z. A. (2011) · Physical Review Letters · doi:10.1103/physrevlett.106.248102 · Cited by 128 · see citing works
Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation
Pulkkinen, O. I., & Metzler, R. (2013) · Physical Review Letters · doi:10.1103/physrevlett.110.198101 · Cited by 120 · see citing works
Natural Agency: The Case of Bacterial Cognition
Fulda, F. C. (2017) · Journal of the American Philosophical Association · doi:10.1017/apa.2017.5 · Cited by 127 · see citing works
Microbial Scout Hypothesis, Stochastic Exit from Dormancy, and the Nature of Slow Growers
Buerger, S. M., Spoering, A. L., Gavrish, E., Leslin, C. M., Ling, L. L., & Epstein, S. S. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07307-11 · Cited by 125 · see citing works
linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cisPreprint
Maamar, H., Cabili, M. N., Rinn, J. L., & Raj, A. (2013) · Genes & Development · doi:10.1101/gad.217018.113 · Cited by 124 · see citing works
Kaiser, M., Jug, F., Julou, T., Deshpande, S., Pfohl, T., Silander, O., Myers, E. W., & van Nimwegen, E. (2018) · Nature Communications · doi:10.1038/s41467-017-02505-0 · Cited by 121 · see citing works
Imaging Transcription in Living Cells
Darzacq, X., Yao, J., Larson, D. R., Causse, S., Bosanac, L., de Turris, V., Ruda, V. M., Lionnet, T., Zenklusen, D., Guglielmi, B., et al. (2009) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.050708.133728 · Cited by 118 · see citing works
A retrospective: Use of Escherichia coli as a vehicle to study phospholipid synthesis and function
Dowhan, W. (2012) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2012.08.007 · Cited by 116 · see citing works
Catalytic Contributions from Remote Regions of Enzyme Structure
Lee, J., & Goodey, N. M. (2011) · Chemical Reviews · doi:10.1021/cr100042n · Cited by 116 · see citing works
BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
Gorochowski, T. E., Matyjaszkiewicz, A., Todd, T., Oak, N., Kowalska, K., Reid, S., Tsaneva-Atanasova, K. T., Savery, N. J., Grierson, C. S., & di Bernardo, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042790 · Cited by 115 · see citing works
Single-Molecule Kinetics in Living Cells
Elf, J., & Barkefors, I. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-110801 · Cited by 109 · see citing works
Stochastic simulation in systems biology
Székely, T., & Burrage, K. (2014) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2014.10.003 · Cited by 108 · see citing works
High-density micro-arrays for mass spectrometry
Urban, P. L., Jefimovs, K., Amantonico, A., Fagerer, S. R., Schmid, T., Mädler, S., Puigmartí‐Luis, J., Goedecke, N., & Zenobi, R. (2010) · Lab on a Chip · doi:10.1039/c0lc00211a · Cited by 109 · see citing works
The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rate
Chu, D., & Barnes, D. J. (2016) · Scientific Reports · doi:10.1038/srep25191 · Cited by 109 · see citing works
Wide lag time distributions break a trade-off between reproduction and survival in bacteria
Moreno-Gámez, S., Kiviet, D. J., Vulin, C., Schlegel, S., Schlegel, K., van Doorn, G. S., & Ackermann, M. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2003331117 · Cited by 109 · see citing works
Membrane heterogeneity – from lipid domains to curvature effects
Semrau, S., & Schmidt, T. (2009) · Soft Matter · doi:10.1039/b901587f · Cited by 108 · see citing works
Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity
Binder, D., Drepper, T., Jaeger, K., Delvigne, F., Wiechert, W., Kohlheyer, D., & Grünberger, A. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.06.009 · Cited by 105 · see citing works
Regulatory consequences of gene translocation in bacteria
Block, D. H. S., Hussein, R., Liang, L. W., & Lim, H. N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks694 · Cited by 105 · see citing works
Optimizing information flow in small genetic networks. II. Feed-forward interactions
Walczak, A. M., Tkačik, G., & Bialek, W. (2010) · Physical Review E · doi:10.1103/physreve.81.041905 · Cited by 100 · see citing works
Exact Results for the Evolution of Stochastic Switching in Variable Asymmetric Environments
Gaál, B., Pitchford, J. W., & Wood, A. J. (2010) · Genetics · doi:10.1534/genetics.109.113431 · Cited by 102 · see citing works
Central Role of the Cell in Microbial Ecology
Zengler, K. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00027-09 · Cited by 102 · see citing works
Cost–benefit theory and optimal design of gene regulation functions
Tomer Kalisky, C., Dekel, E., & Alon, U. S. (2007) · Physical Biology · doi:10.1088/1478-3975/4/4/001 · Cited by 95 · see citing works
Lysogen stability is determined by the frequency of activity bursts from the fate‐determining gene
Zong, C. C., So, L., Sepúlveda, L. A., Skinner, S. O., & Golding, I. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.96 · Cited by 95 · see citing works
Biological role of noise encoded in a genetic network motif
Kittisopikul, M., & Süel, G. M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1003975107 · Cited by 96 · see citing works
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
Roberts, E., Magis, A. T., Ortiz, J. O., Baumeister, W. P., & Luthey-Schulten, Z. A. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002010 · Cited by 99 · see citing works
van Boxtel, C., van Heerden, J. H., Nordholt, N., Schmidt, P., & Bruggeman, F. J. (2017) · Journal of The Royal Society Interface · doi:10.1098/rsif.2017.0141 · Cited by 89 · see citing works
Stochastic Bistability and Bifurcation in a Mesoscopic Signaling System with Autocatalytic Kinase
Bishop, L. M., & Qian, H. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.09.055 · Cited by 93 · see citing works
Transcription Stochasticity of Complex Gene Regulation Models
Schwabe, A., Rybakova, K. N., & Bruggeman, F. J. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.07.011 · Cited by 91 · see citing works
Mean First‐Passage Times in Biology
Polizzi, N. F., Therien, M. J., & Beratan, D. N. (2016) · Israel Journal of Chemistry · doi:10.1002/ijch.201600040 · Cited by 90 · see citing works
Surfing on a new wave of single-molecule fluorescence methods
Hohlbein, J., Gryte, K., Heilemann, M., & Kapanidis, A. N. (2010) · Physical Biology · doi:10.1088/1478-3975/7/3/031001 · Cited by 88 · see citing works
Single-Cell Dynamics Reveals Sustained Growth during Diauxic Shifts
Boulineau, S., Tostevin, F., Kiviet, D. J., ten Wolde, P. R., Nghe, P., & Tans, S. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061686 · Cited by 85 · see citing works
Universal Protein Fluctuations in Populations of Microorganisms
Salman, H., Brenner, N., Tung, C.-K., Elyahu, N., Stolovicki, E., Moore, L., Libchaber, A. J., & Braun, E. (2012) · Physical Review Letters · doi:10.1103/physrevlett.108.238105 · Cited by 83 · see citing works
Ullman, G., Walldén, M., Marklund, E. G., Mahmutovic, A., Razinkov, I., & Elf, J. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0025 · Cited by 83 · see citing works
Control of Stochastic and Induced Switching in Biophysical Networks
Wells, D. K., Kath, W. L., & Motter, A. E. (2015) · Physical Review X · doi:10.1103/physrevx.5.031036 · Cited by 81 · see citing works
Greenfeld, M., Pavlichin, D. S., Mabuchi, H., & Herschlag, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030024 · Cited by 82 · see citing works
Possible origin of life between mica sheets
Hansma, H. G. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.06.016 · Cited by 83 · see citing works
Robinson, A., & van Oijen, A. V. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2994 · Cited by 93 · see citing works
Stochastic Phenotype Transition of a Single Cell in an Intermediate Region of Gene State Switching
Ge, H., Qian, H., & Xie, X. S. (2015) · Physical Review Letters · doi:10.1103/physrevlett.114.078101 · Cited by 79 · see citing works
Self-citationNikel, P. I., Romero–Campero, F. J., Zeidman, J., Goñi‐Moreno, Á., & de Lorenzo, V. (2015) · mBio · doi:10.1128/mbio.00340-15 · Cited by 77 · see citing works
Pre‐dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch
Robert, L., Paul, G., Chen, Y., Taddéi, F., Baigl, D., & Lindner, A. B. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.12 · Cited by 74 · see citing works
Noise Management by Molecular Networks
Bruggeman, F. J., Blüthgen, N., & Westerhoff, H. V. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000506 · Cited by 74 · see citing works
Phenotypic Heterogeneity in Mycobacterium tuberculosis
Dhar, N., McKinney, J. D., & Manina, G. (2016) · Microbiology Spectrum · doi:10.1128/microbiolspec.tbtb2-0021-2016 · Cited by 81 · see citing works
Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity
Qian, H., Shi, P.-Z., & Xing, J. (2009) · Physical Chemistry Chemical Physics · doi:10.1039/b900335p · Cited by 74 · see citing works
Spectral solutions to stochastic models of gene expression with bursts and regulation
Mugler, A., Walczak, A. M., & Wiggins, C. H. (2009) · Physical Review E · doi:10.1103/physreve.80.041921 · Cited by 72 · see citing works
Ferguson, M., Coq, D. L., Jules, M., Aymerich, S., Radulescu, O., Declerck, N., & Royer, C. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110541108 · Cited by 69 · see citing works
Modeling bistable cell-fate choices in theDrosophilaeye: qualitative and quantitative perspectives
Graham, T. G. W., Tabei, S. M. A., Dinner, A. R., & Rebay, I. (2010) · Development · doi:10.1242/dev.044826 · Cited by 68 · see citing works
Tiwari, A., Balázsi, G., Gennaro, M. L., & Igoshin, O. A. (2010) · Physical Biology · doi:10.1088/1478-3975/7/3/036005 · Cited by 69 · see citing works
Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems
Bettenworth, V., Steinfeld, B., Duin, H., Petersen, K., Streit, W. R., Bischofs, I. B., & Becker, A. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.04.036 · Cited by 70 · see citing works
Kondev, J. (2014) · Physics Today · doi:10.1063/pt.3.2276 · Cited by 69 · see citing works
Lipid-dependent Generation of Dual Topology for a Membrane Protein
Bogdanov, M. V., & Dowhan, W. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.404103 · Cited by 69 · see citing works
Wang, Y., Christley, S., Mjolsness, E., & Xie, X. S. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-99 · Cited by 68 · see citing works
Self-citationTransitions in a genetic transcriptional regulatory system under Lévy motion
Zheng, Y., Serdukova, L., Duan, J., & Kurths, J. (2016) · Scientific Reports · doi:10.1038/srep29274 · Cited by 65 · see citing works
Developmental mechanisms underlying variable, invariant and plastic phenotypes
Abley, K., Locke, J. C. W., & Leyser, O. (2016) · Annals of Botany · doi:10.1093/aob/mcw016 · Cited by 64 · see citing works
Effects of Transcriptional Pausing on Gene Expression Dynamics
Rajala, T., Häkkinen, A., Healy, S., Yli-Harja, O. P., & Ribeiro, A. S. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000704 · Cited by 65 · see citing works
- Authors
- Choi, P. J., Cai, L., Frieda, K., & Xie, X. S.
- Affiliations
- Harvard University (US)
- Corresponding author
- Choi, Paul J.
- Cai, Long
- Frieda, Kirsten
- Xie, X. Sunney
- Venue
- Science
- Published
- 2008-10-17
- Volume
- 322
- Issue
- 5900
- Pages
- 442-446
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2819113
- OpenAlex
- W1978182054
- Cited by
- 438
- References
- 28
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 13 · 2023: 11 · 2022: 11 · 2021: 14 · 2020: 21 · 2019: 33 · 2018: 28 · 2017: 26 · 2016: 30 · 2015: 27 · 2014: 35 · 2013: 34 · 2012: 37
- FWCI
- 19.62
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- National Institutes of Health (DP1OD000277)
- National Institute of Biomedical Imaging and Bioengineering (R01EB010244)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Keywords
- lac operon, lactose permease, lactose repressor, phenotypic switching, stochastic gene expression, single-molecule fluorescence, Escherichia coli, basal expression, gene expression regulation
- MeSH terms
- Bacterial Proteins, Escherichia coli, Lac Operon, Lactose, Microscopy, Fluorescence, Models, Genetic, Monosaccharide Transport Proteins, Operator Regions, Genetic, Phenotype, Recombinant Fusion Proteins, Repressor Proteins, RNA, Messenger, Stochastic Processes, Gene Expression Regulation, Bacterial, Feedback, Physiological, Symporters, Escherichia coli Proteins, Lac Repressors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review