Russian version English version
Volume 11   Issue 1   Year 2016
Likhoshvai V.A., Khlebodarova T.M.

Phenotypic Variability of Bacterial Cell Cycle: Mathematical Model

Mathematical Biology & Bioinformatics. 2016;11(1):91-113.

doi: 10.17537/2016.11.91.



  1. Ferrell J.E.Jr. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell. Biol. 2002;14:140-148. doi: 10.1016/S0955-0674(02)00314-9
  2. Angeli D., Ferrell J.E. Jr., Sontag E.D. Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl. Acad. Sci. USA. 2004;101:1822-1827. doi: 10.1073/pnas.0308265100
  3. Ozbudak E.M., Thattai M., Lim H.N., Shraiman B.I., Van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature. 2004;427(6976):737-740. doi: 10.1038/nature02298
  4. Smits W.K., Kuipers O.P., Veening J.W. Phenotypic variation in bacteria: the role of feedback regulation. Nat. Rev. Microbiol. 2006;4(4):259-271. doi: 10.1038/nrmicro1381
  5. Dubnau D., Losick R. Bistability in bacteria. Mol. Microbiol. 2006;61:564-572. doi: 10.1111/j.1365-2958.2006.05249.x
  6. Piggot P. Epigenetic switching: bacteria hedge bets about staying or moving. Curr. Biol. 2010;20(11):R480-482. doi: 10.1016/j.cub.2010.04.020
  7. Avendaño M.S., Leidy C., Pedraza J.M. Tuning the range and stability of multiple phenotypic states with coupled positive-negative feedback loops. Nat. Commun. 2013;4. Article No 2605. doi: 10.1038/ncomms3605
  8. Kaern M., Elston T.C., Blake W.J., Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 2005;6:451-464. doi: 10.1038/nrg1615
  9. Sureka K., Ghosh B., Dasgupta A., Basu J., Kundu M., Bose I. Positive feedback and noise activate the stringent response regulator rel in mycobacteria. PLoS One. 2008;3(3). Article No e1771.
  10. To T.L., Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science. 2010;327(5969):1142-1145. doi: 10.1126/science.1178962
  11. Zheng X.D., Yang X.Q., Tao Y. Bistability, probability transition rate and first-passage time in an autoactivating positive-feedback loop. PLoS One. 2011;6(3). Article No e17104. doi: 10.1371/journal.pone.0017104
  12. Shu C.C., Chatterjee A., Dunny G., Hu W.S., Ramkrishna D. Bistability versus bimodal distributions in gene regulatory processes from population balance. PLoS Comput. Biol. 2011;7(8). Article No e1002140. doi: 10.1371/journal.pcbi.1002140
  13. Ghosh S., Banerjee S., Bose I. Emergent bistability: Effects of additive and multiplicative noise. Eur. Phys. J. E Soft. Matter. 2012;35:11. doi: 10.1140/epje/i2012-12011-4
  14. Thomas P., Popović N., Grima R. Phenotypic switching in gene regulatory networks. Proc. Natl. Acad. Sci. USA. 2014;111(19):6994-6999. doi: 10.1073/pnas.1400049111
  15. Casadesús J., Low D.A. Programmed heterogeneity: epigenetic mechanisms in bacteria. J. Biol. Chem. 2013;288:13929-13935. doi: 10.1074/jbc.R113.472274
  16. Stewart E.J., Madden R., Paul G., Taddei F. Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol. 2005;3(2):e45. doi: 10.1371/journal.pbio.0030045
  17. Ghosh S., Sureka K., Ghosh B., Bose I., Basu J., Kundu M. Phenotypic heterogeneity in mycobacterial stringent response. BMC Syst. Biol. 2011;5:18. doi: 10.1186/1752-0509-5-18
  18. Kotte O., Volkmer B., Radzikowski J.L., Heinemann M. Phenotypic bistability in Escherichia coli's central carbon metabolism. Mol. Syst. Biol. 2014;10:736. doi: 10.15252/msb.20135022
  19. Klapper I., Gilbert P., Ayati B.P., Dockery J., Stewart P.S. Senescence can explain microbial persistence. Microbiology. 2007;153:3623-3630. doi: 10.1099/mic.0.2007/006734-0
  20. Balaban N.Q., Merrin J., Chait R., Kowalik L., Leibler S. Bacterial persistence as a phenotypic switch. Science. 2004;305:1622-1625. doi: 10.1126/science.1099390
  21. Verstraeten N., Knapen W., Fauvart M., Michiels J. A Historical Perspective on Bacterial Persistence. Methods Mol. Biol. 2016;1333:3-13. doi: 10.1007/978-1-4939-2854-5_1
  22. Dörr T., Vulić M., Lewis K. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol. 2010;8(2). Article No e1000317. doi: 10.1371/journal.pbio.1000317
  23. Fasani R.A., Savageau M.A. Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype. Proc. Natl. Acad. Sci. USA. 2013;110:E2528-2537. doi: 10.1073/pnas.1301023110
  24. Gelens L., Hill L., Vandervelde A., Danckaert J., Loris R. A general model for toxin-antitoxin module dynamics can explain persister cell formation in E. coli. PLoS Comput. Biol. 2013;9. Article No e1003190. doi: 10.1371/journal.pcbi.1003190
  25. Likhoshvai V.A., Khlebodarova T.M. Coordination of cell growth and DNA replication: A mathematical model. Mathematical Biology and Bioinformatics. 2013;8(1):66-92 (in Russ.). doi: 10.17537/2013.8.66
  26. Likhoshvai V.A., Khlebodarova T.M. Mathematical modeling of bacterial cell cycle: The problem of coordinating genome replication with cell growth. J. Bioinform. Comput. Biol. 2014;12(3). Article No. 1450009. doi: 10.1142/S0219720014500097
  27. Donachie W.D. Relationship between cell size and time of initiation of DNA replication. Nature. 1968;219:1077-1079. doi: 10.1038/2191077a0
  28. Cooper S., Helmstetter C.E. Chromosome replication and the division cycle of Escherichia coli B/r. J. Mol. Biol. 1968;31:619-644. doi: 10.1016/0022-2836(68)90425-7
  29. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Ed. Neidhardt F.C. Washington D.C.: American Society for Microbiology; 1987. 1654 p.
  30. Kennell D., Riezman H. Transcription and translation initiation frequencies of the Escherichia coli lac operon. J. Mol. Biol. 1977;114:1-21. doi: 10.1016/0022-2836(77)90279-0
  31. Zaritsky A., Woldringh C.L. Chromosome replication rate and cell shape in Escherichia coli: lack of coupling. J. Bacteriol. 1978;135(2):581-587.
  32. Pedersen S., Reeh S., Friesen, D.J. Functional mRNA half-lives in E. coli. Mol. Gen. Genet. 1978;166:329-336.
  33. Mosteller R.D., Goldstein R.V., Nishimoto K.R. Metabolism of individual proteins in exponentially growing Escherichia coli. J. Biol. Chem. 1980;255(6):2524-2532.
  34. Selinger D.W., Saxena R.M., Cheung K.J., Church G.M., Rosenow C. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 2003;13(2):216-223. doi: 10.1101/gr.912603
  35. Bernstein J.A., Lin P.H., Cohen S.N., Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. USA. 2004;101(9):2758-2763. doi: 10.1073/pnas.0308747101
  36. Jayapal K.P., Sui S., Philp R.J., Kok Y.J., Yap M.G., Griffin T.J., Hu W.S. Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems. J. Proteome Res. 2010;9(5):2087-2097. doi: 10.1021/pr9007738
  37. 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. 2010;329(5991):533-538. doi: 10.1126/science.1188308
  38. Inouye M., Shaw J., Shen C. The assembly of a structural lipoprotein in the envelope of Escherichia coli. J. Biol. Chem. 1972;247(24):8154-8159.
  39. Schaechter M., Maaloe O., Kjeldgaard N.O. Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. J. Gen. Microbiol. 1958;19:592-606. doi: 10.1099/00221287-19-3-592
  40. Schaechter M., Williamson J.P., Hood J.R. Jr., Koch A.L. Growth, cell and nuclear divisions in some bacteria. J. Gen. Microbiol. 1962;29:421-434. doi: 10.1099/00221287-29-3-421
  41. Yoshikawa H., O'Sullivan A., Sueoka N. Sequential replication of the Bacillus subtilis chromosome. III. Regulation of initiation. Proc. Natl. Acad. Sci. USA. 1964;52:973-980. doi: 10.1073/pnas.52.4.973
  42. Zaritsky A., Vischer N., Rabinovitch A. Changes of initiation mass and cell dimensions by the 'eclipse'. Mol. Microbiol. 2007;63:15-21. doi: 10.1111/j.1365-2958.2006.05501.x
  43. Zaritsky A., Wang P., Vischer N.O. Instructive simulation of the bacterial cell division cycle. Microbiology. 2011;157:1876-1885. doi: 10.1099/mic.0.049403-0
  44. Grant M.A., Saggioro C., Ferrari U., Bassetti B., Sclavi B., Cosentino Lagomarsino M. DnaA and the timing of chromosome replication in Escherichia coli as a function of growth rate. BMC Syst. Biol. 2011;5:201. doi: 10.1186/1752-0509-5-201
  45. Soo V.W., Cheng H.Y., Kwan B.W., Wood T.K. De novo synthesis of a bacterial toxin/antitoxin system. Sci. Rep. 2014;4:4807. doi: 10.1038/srep04807
  46. Keren I., Shah D., Spoering A., Kaldalu N., Lewis K. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J. Bacteriol. 2004;186:8172-8180. doi: 10.1128/JB.186.24.8172-8180.2004
  47. Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., Lewis K. Persisters: a distinct physiological state of E. coli. BMC Microbiol. 2006;6:53. doi: 10.1186/1471-2180-6-53
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2016.11.91
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References Translation into English
Math. Biol. Bioinf.
doi: 10.17537/2017.12.t23

Full text (eng., pdf)


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