Transcriptional delay stabilizes bistable gene networks

Physical Review Letters

Volumn 111, Issue 5, 2013, Pages

  Gupta, Chinmaya ^a   López, José Manuel ^a   Ott, William ^a   Josić, Krešimir ^a   Bennett, Matthew R ^b  

^a University of Houston   (United States)

^b RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BISTABLE SYSTEM; BISTABLES; GENE NETWORKS; MEAN RESIDENCE TIME; NON-MARKOVIAN; REDUCED MODEL; STABLE STATE;

ATOMIC PHYSICS; PHYSICS;

GENES;

ALGORITHM; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION;

ALGORITHMS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; MODELS, GENETIC; TRANSCRIPTION, GENETIC;

EID: 84881535742     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.111.058104     Document Type: Article

References (41)

1. H. H. McAdams and L. Shapiro, Science 269, 650 (1995). SCIEAS 0036-8075 10.1126/science.7624793
2. P. Smolen, D. A. Baxter, and J. H. Byrne, Biophys. J. 83, 2349 (2002). BIOJAU 0006-3495 10.1016/S0006-3495(02)75249-1
3. W. Mather, M. R. Bennett, J. Hasty, and L. S. Tsimring, Phys. Rev. Lett. 102, 068105 (2009). PRLTAO 0031-9007 10.1103/PhysRevLett.102.068105
4. K. Josić, W. Ott, J. M. Lopez, L.-J. Shiau, and M. R. Bennett, PLoS Comput. Biol. 7, e1002264 (2011). PCBLBG 1553-7358 10.1371/journal.pcbi. 1002264
5. O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochemistry 20, 6929 (1981). BICHAW 0006-2960 10.1021/bi00527a028
6. G.-W. Li, O. G. Berg, and J. Elf, Nat. Phys. 5, 294 (2009). NPAHAX 1745-2473 10.1038/nphys1222
7. A. Amir, S. Meshner, T. Beatus, and J. Stavans, Mol. Microbiol. 76, 428 (2010). MOMIEE 0950-382X 10.1111/j.1365-2958.2010.07111.x
8. B. C. Goodwin, Adv. Enzyme Regul. 3, 425 (1965). AEZRA2 0065-2571 10.1016/0065-2571(65)90067-1
9. J. Lewis, Curr. Biol. 13, 1398 (2003). CUBLE2 0960-9822 10.1016/S0960-9822(03)00534-7 (Pubitemid 37029429)
10. N. A. Monk, Curr. Biol. 13, 1409 (2003). CUBLE2 0960-9822 10.1016/S0960-9822(03)00494-9 (Pubitemid 37029430)
11. P. Smolen, D. A. Baxter, and J. H. Byrne, Am. J. Physiol. 277, C777 (1999). AJPHAP 0002-9513
12. K. Sriram and M. S. Gopinathan, J. Theor. Biol. 231, 23 (2004). JTBIAP 0022-5193 10.1016/j.jtbi.2004.04.006 (Pubitemid 39201034)
13. M. Ukai-Tadenuma, R. G. Yamada, H. Xu, J. A. Ripperger, A. C. Liu, and H. R. Ueda, Cell 144, 268 (2011). CELLB5 0092-8674 10.1016/j.cell.2010.12.019
14. J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty, Nature (London) 456, 516 (2008). NATUAS 0028-0836 10.1038/nature07389 (Pubitemid 352759003)
15. M. Tigges, T. T. Marquez-Lago, J. Stelling, and M. Fussenegger, Nature (London) 457, 309 (2009). NATUAS 0028-0836 10.1038/nature07616
16. T. Hong, J. Xing, L. Li, and J. J. Tyson, BMC Syst. Biol. 6, 66 (2012). 1752-0509 10.1186/1752-0509-6-66
17. E. He, O. Kapuy, R. A. Oliveira, F. Uhlmann, J. J. Tyson, and B. Novák, Proc. Natl. Acad. Sci. U.S.A. 108, 10 016 (2011). PNASA6 0027-8424 10.1073/pnas.1102106108
18. E. M. Ozbudak, M. Thattai, H. N. Lim, B. I. Shraiman, and A. van Oudenaarden, Nature (London) 427, 737 (2004). NATUAS 0028-0836 10.1038/nature02298 (Pubitemid 38294592)
19. T. B. Kepler and T. C. Elston, Biophys. J. 81, 3116 (2001). BIOJAU 0006-3495 10.1016/S0006-3495(01)75949-8
20. E. Aurell and K. Sneppen, Phys. Rev. Lett. 88, 048101 (2002). PRLTAO 0031-9007 10.1103/PhysRevLett.88.048101
21. P. B. Warren and P. R. ten Wolde, J. Phys. Chem. B 109, 6812 (2005). JPCBFK 1520-6106 10.1021/jp045523y (Pubitemid 40538450)
22. N. Q. Balaban, J. Merrin, R. Chait, L. Kowalik, and S. Leibler, Science 305, 1622 (2004). SCIEAS 0036-8075 10.1126/science.1099390 (Pubitemid 39296357)
23. T. S. Gardner, C. R. Cantor, and J. J. Collins, Nature (London) 403, 339 (2000). NATUAS 0028-0836 10.1038/35002131 (Pubitemid 30062394)
24. D. Nevozhay, R. M. Adams, E. Van Itallie, M. R. Bennett, and G. Balázsi, PLoS Comput. Biol. 8, e1002480 (2012). PCBLBG 1553-7358 10.1371/journal.pcbi.1002480
25. D. Bratsun, D. Volfson, L. S. Tsimring, and J. Hasty, Proc. Natl. Acad. Sci. U.S.A. 102, 14 593 (2005). PNASA6 0027-8424 10.1073/pnas.0503858102 (Pubitemid 41457102)
26. A. Grönlund, P. Lötstedt, and J. Elf, Proc. Natl. Acad. Sci. U.S.A. 107, 8171 (2010). PNASA6 0027-8424 10.1073/pnas.0913317107
27. R. Maithreye, R. R. Sarkar, V. Parnaik, and S. Sinha, PLoS One 3, e2972 (2008). POLNCL 1932-6203 10.1371/journal.pone.0002972
28. M. Scott, Phys. Rev. E 80, 031129 (2009). PLEEE8 1539-3755 10.1103/PhysRevE.80.031129
29. C. Wang, M. Yi, and K. Yang, in Proceedings of the 2011 IEEE International Conference on Systems Biology (ISB) (IEEE, New York, 2011), pp. 101-110.
30. I. B. Schwartz, T. W. Carr, L. Billings, and M. Dykman, arXiv:1207.7278v1.
31. Z.-L. Jia, Chin. Phys. Lett. 25, 2860 (2008). CPLEEU 0256-307X 10.1088/0256-307X/25/8/035
32. J. Lei, G. He, H. Liu, and Q. Nie, Nonlinearity 22, 2845 (2009). NONLE5 0951-7715 10.1088/0951-7715/22/12/003
33. C.-J. Wang, Int. J. Mod. Phys. B 27, 1350085 (2013). IJPBEV 0217-9792 10.1142/S0217979213500859
34. R. Schlicht and G. Winkler, J. Math. Biol. 57, 613 (2008). JMBLAJ 0303-6812 10.1007/s00285-008-0178-y
35. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.111.058104 for the case of distributed delays and delayed degradation. It also contains details of the numerical implementations for all models, and the stability analysis for the deterministic counterpart to the single-gene, positive feedback system.
36. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990). RMPHAT 0034-6861 10.1103/RevModPhys.62.251
37. L. S. Tsimring and A. Pikovsky, Phys. Rev. Lett. 87, 250602 (2001). PRLTAO 0031-9007 10.1103/PhysRevLett.87.250602
38. C. Masoller, Phys. Rev. Lett. 90, 020601 (2003). PRLTAO 0031-9007 10.1103/PhysRevLett.90.020601
39. M. Fischer and P. Imkeller, Stoch. Dyn. 05, 247 (2005). 0219-4937 10.1142/S0219493705001389 (Pubitemid 44103067)
40. T. Brett and T. Galla, Phys. Rev. Lett. 110, 250601 (2013). PRLTAO 0031-9007 10.1103/PhysRevLett.110.250601
41. T. Tian, K. Burrage, P. M. Burrage, and M. Carletti, J. Comput. Appl. Math. 205, 696 (2007). JCAMDI 0377-0427 10.1016/j.cam.2006.02.063 (Pubitemid 46719713)