Competition for catalytic resources alters biological network dynamics

Physical Review Letters

Volumn 108, Issue 1, 2012, Pages

  Rondelez, Yannick ^a  

^a INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; CELLULAR BEHAVIORS; COMPETITION EFFECTS; CROSS-COUPLINGS; DIFFERENT SUBSTRATES; DYNAMIC OPERATIONS; ENZYME SATURATION; EXPERIMENTAL MODELS; EXPERIMENTAL SYSTEM; GENE-EXPRESSION MACHINERY; GENETIC REGULATION; GLOBAL DYNAMICS; NETWORK FUNCTIONS; REGULATORY INTERACTIONS; SYNTHETIC BIOLOGY;

DYNAMICS; GENE EXPRESSION; MACHINERY; SUBSTRATES;

ENZYMES;

EID: 84855481443     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.108.018102     Document Type: Article

References (34)

1. E.H. Davidson, Nature (London) NATUAS 0028-0836 468, 911 (2010). 10.1038/nature09645
2. A. Goldbeter, Biochemical Oscillations and Cellular Rhythms (Cambridge University Press, Cambridge, 1996).
3. S. Widder, J. Macía, and R. Solé, PLoS ONE 4, e5399 (2009). 1932-6203 10.1371/journal.pone.0005399
4. R. Silva-Rocha and V. de Lorenzo, FEBS Lett. 582, 1237 (2008); FEBLAL 0014-5793 10.1016/j.febslet.2008.01.060
5. D. Nevhozay, Proc. Natl. Acad. Sci. U.S.A. 106, 5123 (2009). PNASA6 0027-8424 10.1073/pnas.0809901106
6. M.B. Elowitz and S. Leibler, Nature (London) NATUAS 0028-0836 403, 335 (2000). 10.1038/35002125 (Pubitemid 30062393)
7. T.S. Gardner, C.R. Cantor, and J.J. Collins, Nature (London) NATUAS 0028-0836 403, 339 (2000). 10.1038/35002131 (Pubitemid 30062394)
8. J.C. Anderson, C.A. Voigt, and A.P. Arkin, Mol. Syst. Biol. 3, 133 (2007). MSBOC3 1744-4292 10.1038/msb4100173 (Pubitemid 47258528)
9. Q. Thommen, PLoS Comput. Biol. 6, e1000990 (2010). PCBLBG 1553-7358 10.1371/journal.pcbi.1000990
10. J.J. Tyson, K.C. Chen, and B. Novak, Curr. Opin. Cell Biol. COCBE3 0955-0674 15, 221 (2003). 10.1016/S0955-0674(03)00017-6 (Pubitemid 36332198)
11. D. Sprinzak and M.B. Elowitz, Nature (London) NATUAS 0028-0836 438, 443 (2005). 10.1038/nature04335 (Pubitemid 41742009)
12. Other types of competition-that do not involve catalysis-can occur in genetic regulation, e.g., competition of transcription factors for overlapping binding sites. See for example: R. Hermsen, S. Tans, and P.R. ten Wolde, PLoS Comput. Biol. 2, e164 (2006). PCBLBG 1553-734X 10.1371/journal.pcbi.0020164 (Pubitemid 46045168)
13. P. Kim and B. Tidor, Genome Res. 13, 2391 (2003). GEREFS 1088-9051 10.1101/gr.1207003 (Pubitemid 37428262)
14. J. Kim, J.J. Hopfield, and E. Winfree, in Advances in Neural Information Processing Systems (NIPS), edited by, L. Saul, Y. Weiss, and, L. Bottou, (MIT Press, Cambridge, MA, 2005), Vol. 17, p. 681, http://books.nips.cc/papers/files/ nips17/NIPS2004-0247.pdf.
15. W.H. Mather, N.A. Cookson, J. Hasty, L.S. Tsimring, and R.J. Williams, Biophys. J. 99, 3172 (2010); BIOJAU 0006-3495 10.1016/j.bpj.2010.09.057
16. N. Nandagopal and M. Elowitz Science 333, 1244 (2011). SCIEAS 0036-8075 10.1126/science.1207084
17. C. Tan, P. Marguet, and L. You, Nat. Chem. Biol. 5, 842 (2009). NCBABT 1552-4450 10.1038/nchembio.218
18. W.W. Wong, T.Y. Tsai, and J.C. Liao, Mol. Syst. Biol. 3, 130 (2007). MSBOC3 1744-4292 10.1038/msb4100172 (Pubitemid 47196779)
19. E. Fung, W.W. Wong, J.K. Suen, T. Bulter, S. Lee, and J.C. Liao, Nature (London) NATUAS 0028-0836 435, 118 (2005). 10.1038/nature03508 (Pubitemid 40655919)
20. J. Stricker, Nature (London) NATUAS 0028-0836 456, 516 (2008). 10.1038/nature07389 (Pubitemid 352759003)
21. S. Basu, Y. Gerchman, C.H. Collins, F.H. Arnold, and R. Weiss, Nature (London) NATUAS 0028-0836 434, 1130 (2005). 10.1038/nature03461 (Pubitemid 40663491)
22. N.E. Buchler, U. Gerland, and T. Hwa, Proc. Natl. Acad. Sci. U.S.A. 102, 9559 (2005). PNASA6 0027-8424 10.1073/pnas.0409553102 (Pubitemid 40981720)
23. G. Kurosawa and Y. Iwasa, J. Biol. Rhythms JBRHEE 0748-7304 17, 568 (2002). 10.1177/0748730402238239 (Pubitemid 37187319)
24. A. Zaslaver, PLoS Comput. Biol. 5, e1000545 (2009); PCBLBG 1553-7358 10.1371/journal.pcbi.1000545
25. M.R. Maurizi, Cell. Mol. Life Sci. 48, 178 (1992); EXPEAM 0014-4754 10.1007/BF01923511
26. E. Dervyn, D. Canceill, and O. Huisman, J. Bacteriol. 172, 7098 (1990), http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210832/. JOBAAY 0021-9193
27. P. Marguet, Y. Tanouchi, E. Spitz, C. Smith, and L. You, PLoS ONE 5, e11909 (2010). POLNCL 1932-6203 10.1371/journal.pone.0011909
28. K.L. Jones, S.-W. Kim, and J.D. Keasling, Metab. Eng. 2, 328 (2000). MEENFM 1096-7176 10.1006/mben.2000.0161 (Pubitemid 32122506)
29. A. Farewell, K. Kvint, and T. Nystrom, Mol. Microbiol. 29, 1039 (1998); MOMIEE 0950-382X 10.1046/j.1365-2958.1998.00990.x (Pubitemid 28389444)
30. H. Maeda, N. Fujita, and A. Ishihama, Nucleic Acids Res. NARHAD 0305-1048 28, 3497 (2000). 10.1093/nar/28.18.3497
31. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.108.018102 for mathematical details on models used in this letter.
32. J. Kim and E. Winfree, Mol. Syst. Biol. 7, 465 (2011); MSBOC3 1744-4292 10.1038/msb.2010.119
33. K. Montagne, R. Plasson, Y. Sakai, T. Fujii, and Y. Rondelez, Mol. Syst. Biol. 7, 466 (2011); MSBOC3 1744-4292 10.1038/msb.2010.120
34. E. Karzbrun, J. Shin, R.H. Bar-Ziv, and V. Noireaux, Phys. Rev. Lett. 106, 048104 (2011). PRLTAO 0031-9007 10.1103/PhysRevLett.106.048104