Sequestration-based bistability enables tuning of the switching boundaries and design of a latch

Molecular Systems Biology

Volumn 8, Issue , 2012, Pages

  Chen, David ^a,b   Arkin, Adam P ^b,c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California at Berkeley   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

bistability; genetic circuits; nonlinear dynamics; sequestration; synthetic biology

Indexed keywords

SIGMA FACTOR;

ARTICLE; BISTABLE SWITCH; CONTROLLED STUDY; GENE SEGREGATION; GENE SWITCHING; MOLECULAR DYNAMICS; MOLECULAR STABILITY; NONHUMAN; NONLINEAR SYSTEM; POSITIVE FEEDBACK; PREDICTION; PRIORITY JOURNAL; SYNTHETIC BIOLOGY; BACILLUS SUBTILIS; BACTERIAL GENE; ESCHERICHIA COLI; FEEDBACK SYSTEM; GENETICS; REGULATOR GENE;

BACILLUS SUBTILIS; ESCHERICHIA COLI; FEEDBACK, PHYSIOLOGICAL; GENES, BACTERIAL; GENES, SWITCH;

EID: 84868279233     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2012.52     Document Type: Article

References (41)

1. Acar M, Becskei A, van Oudenaarden A (2005) Enhancement of cellular memory by reducing stochastic transitions. Nature 435: 228-232 (Pubitemid 40685951)
2. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EPS, Landgraf D, Phillips I, Silver PA (2007) Rational design of memory in eukaryotic cells. Genes Dev 21: 2271-2276 (Pubitemid 47443332)
3. Angeli D, Ferrell JE, Sontag ED (2004) Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci USA 101: 1822-1827 (Pubitemid 38228975)
4. Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113: 597-607 (Pubitemid 36694185)
5. Bashor CJ, Helman NC, Yan S, Lim WA (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319: 1539-1543 (Pubitemid 351398185)
6. Becskei A, Seraphin B, Serrano L (2001) Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J 20: 2528-2535 (Pubitemid 32452871)
7. Bonnet J, Subsoontorn P, Endy D (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality. PNAS 109: 8884-8889
8. Buchler NE, Cross FR (2009) Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol Syst Biol 5: 272
9. Buchler NE, Louis M (2008) Molecular titration and ultrasensitivity in regulatory networks. J Mol Biol 384: 1106-1119
10. Burrill DR, Silver PA (2010) Making cellular memories. Cell 140: 13-18
11. Cox RS, Dunlop MJ, Elowitz MB (2010) A synthetic three-color scaffold for monitoring genetic regulation and noise. J Biol Eng 4: 10
12. Ferrell JE (1996) Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 21: 460-466
13. Ferrell JE (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14: 140-148
14. Francois P, Hakim V (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci USA 101: 580-585 (Pubitemid 38084679)
15. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ (2009) Synthetic gene networks that count. Science 324: 1199-1202
16. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (Pubitemid 30062394)
17. Ham TS, Lee SK, Keasling JD, Arkin AP (2008) Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS ONE 3: e2815
18. Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, Keasling JD (2001) Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology 147: 3241-3247 (Pubitemid 33150330)
19. Kim SY, Ferrell Jr JE (2007) Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell 128: 1133-1145 (Pubitemid 46437260)
20. Kim J, White KS, Winfree E (2006) Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol 2: 68
21. Klumpp S, Zhang Z, Hwa T (2009) Growth rate-dependent global effects on gene expression in bacteria. Cell 139: 1366-1375
22. Kramer BP, Fussenegger M (2005) Hysteresis in a synthetic mammalian gene network. Proc Natl Acad Sci USA 102: 9517-9522 (Pubitemid 40981713)
23. Lane WJ, Darst SA (2006) The structural basis for promoter-35 element recognition by the group IV factors. PLoS Biol 4: e269
24. Lee T-H, Maheshri N (2012) A regulatory role for repeated decoy transcription factor binding sites in target gene expression. Mol Syst Biol 8: 576
25. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Meth 4: 251-256 (Pubitemid 46358876)
26. Lou C, Liu X, Ni M, Huang Y, Huang Q, Huang L, Jiang L, Lu D, Wang M, Liu C, Chen D, Chen C, Chen X, Yang L, Ma H, Chen J, Ouyang Q (2010) Synthesizing a novel genetic sequential logic circuit: A push-on push-off switch. Mol Syst Biol 6: 350
27. Lu MS, Mauser JF, Prehoda KE (2011) Ultrasensitive synthetic protein regulatory networks using mixed decoys. ACS Synth Biol 1: 65-72
28. Nevozhay D, Adams RM, Van Itallie E, Bennett MR, Balázsi G (2012) Mapping the environmental fitness landscape of a synthetic gene circuit. PLoS Comput Biol 8: e1002480
29. Newman JD, Anthony JR, Donohue TJ (2001) The importance of zinc-binding to the function of Rhodobacter sphaeroides ChrR as an anti-sigma factor. J Mol Biol 313: 485-499 (Pubitemid 33052282)
30. Ozbudak EM, Thattai M, Lim HN, Shraiman BI, van Oudenaarden A (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427: 737-740 (Pubitemid 38294592)
31. Palani S, Sarkar CA (2011) Synthetic conversion of a graded receptor signal into a tunable, reversible switch. Mol Syst Biol 7: 480
32. Qiu J, Helmann JD (2001) The {-}10 region is a key promoter specificity determinant for the Bacillus subtilis extracytoplasmic-function {sigma} factors {sigma}X and {sigma}W. J Bacteriol 183: 1921-1927 (Pubitemid 32225986)
33. Ray JCJ, Tabor JJ, Igoshin OA (2011) Non-transcriptional regulatory processes shape transcriptional network dynamics. Nat Rev Microbiol 9: 817-828
34. Schilke BA, Donohue TJ (1995) ChrR positively regulates transcription of the Rhodobacter sphaeroides cytochrome c2 gene. J. Bacteriol 177: 1929-1937
35. Schöbel S, Zellmeier S, Schumann W, Wiegert T (2004) The Bacillus subtilissW anti-sigma factor RsiW is degraded by intramembrane proteolysis through YluC. Mol Microbiol 52: 1091-1105 (Pubitemid 38916176)
36. Staroń A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T (2009) The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) s factor protein family. Mol Microbiol 74: 557-581
37. Tan C, Marguet P, You L (2009) Emergent bistability by a growth-modulating positive feedback circuit. Nat Chem Biol 5: 842-848
38. Tiwari A, Balázsi G, Gennaro ML, Igoshin OA (2010) The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Phys Biol 7: 036005
39. Trunnell NB, Poon AC, Kim SY, Ferrell Jr JE (2011) Ultrasensitivity in the regulation of Cdc25C by Cdk1. Mol Cell 41: 263-274
40. Wang Q, Niemi J, Tan C, You L, West M(2010) Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy. Cytometry A 77A: 101-110
41. Zellmeier S, Schumann W, Wiegert T (2006) Involvement of Clp protease activity in modulating the Bacillus subtilissW stress response. Mol Microbiol 61: 1569-1582 (Pubitemid 44359384)