Ground state robustness as an evolutionary design principle in signaling networks

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  Kartal, Önder ^a,b   Ebenhöh, Oliver ^a,b,c  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b UNIVERSITY OF POTSDAM   (Germany)

^c UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; KINETICS; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

EID: 77953998498     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008001     Document Type: Article

References (44)

1. Friedman A, Perrimon N (2007) Genetic screening for signal transduction in the era of network biology. Cell 128: 225-231.
2. Wagner A (2003) Does selection mold molecular networks? Sci STKE pe41.
3. Wagner A (2008) Neutralism and selectionism: a network based reconciliation. Nature Reviews Genetics 9: 965-974.
4. Stelling J, Sauer U, Szallasi Z, Doyle FJ, Doyle J (2004) Robustness of cellular functions. Cell 118: 675-685.
5. Kitano H (2004) Biological robustness. Nature Reviews Genetics 5: 826-837.
6. Hammerstein P, Hagen EH, Herz AVM, Herzel H (2006) Robustness: a key to evolutionary design. Biological Theory 1: 90-93.
7. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
8. Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387: 913-917.
9. Alon U, Surette MG, Barkai N, Leibler S (1999) Robustness in bacterial chemotaxis. Nature 397: 168-171.
10. Kollmann M, Løvdok L, Bartholomé K, Timmer J, Sourjik V (2005) Design principles of a bacterial signaling network. Nature 438: 504-507.
11. Albert R, Jeong H, Barabási AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382.
12. Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nature Reviews Genetics 5: 101-114.
13. Prill RJ, Iglesias PA, Levchenko A (2005) Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 3: e343.
14. Soyer OS, Salathé M, Bonhoeffer S (2006) Signal transduction networks: topology, response and biochemical processes. Journal of Theoretical Biology 238: 416-425.
15. Heinrich R, Neel BG, Rapoport TA (2002) Mathematical models of protein kinase signal transduction. Molecular Cell 9: 957-970.
16. Binder B, Heinrich R (2004) Interrelations between dynamical properties and structural characteristics of signal transduction networks. Genome Informatics 15: 13-23.
17. Binder B, Heinrich R (2005) Structural and dynamical analysis of the kinase network derived from the transpath database. Genome Informatics 16: 164-173.
18. Cvětkovic DM, Doob M, Sachs H (1995) Spectra of graphs. Johann Ambrosius Barth.
19. Gleich DF. Matlab BGL 4. 0. Available: http://www.stanford.edu/,dgleich/programs/matlab_bgl/. Accessed 2009 Jul 1.
20. Bang-Jensen J, Gutin G (2001) Digraphs: theory, algorithms and applications. Springer.
21. Alon N, Yuster R, Zwick U (1995) Color-coding. J ACM 42: 844-856.
22. Horn R, Johnson CR (1999) Matrix analysis. Cambridge University Press.
23. Cooper CDH (1973) On the maximum eigenvalue of a reducible non-negative real matrix. Math Z 131: 213-217.
24. Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283: 381-387.
25. Brualdi RA (1982) Matrices, eigenvalues and directed graphs. Linear and Multilinear Algebra 11: 143-165.
26. Zhang XD, Li JS (2002) Spectral radius of non-negative matrices and digraphs. Acta Mathematica Sinica 18: 293-300.
27. Ebenhöh O, Heinrich R (2003) Stoichiometric design of metabolic networks: Multifunctionality, clusters, optimization, weak and strong robustness. Bull Math Biol 65: 323-357.
28. Wagner A (2003) How the global structure of protein interaction networks evolves. Proceedings of the Royal Society London B 270: 457-466.
29. Bhattacharyya RP, Reményi A, Yeh BJ, Lim WA (2006) Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annual Review of Biochemistry 75: 655-680.
30. Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300: 445-452.
31. Piao X, Paulson R, Van Der Geer P, Pawson T, Bernstein A (1996) Oncogenic mutation in the kit receptor tyrosine kinase alters substrate specificity and induces degradation of the protein tyrosine phosphatase shp-1. Proceedings of the National Academy of Sciences 93: 14665-14669.
32. Songyang Z, Carraway KL III, Eck MJ, Harrison SC, Feldman RA, et al. (1995) Catalytic specificity of protein-tyrosine kinases is critical for selective signaling. Nature 373: 536-539.
33. Choi C, Krull M, Kel A, Kel-Margoulis O, Pistor S, et al. (2004) TRANSPATH - a high quality database focused on signal transduction. Comp Funct Genomics 5: 163-168.
34. Kobilka BK, Xiang Y. Adrenergic pathway. Sci. Signal. Available: http://stke.sciencemag.org/cgi/cm/stkecm;CMP_8762. Accessed 2009 Sep 10.
35. Cambier JC, Gauld SB, Dal Porto JM. B cell antigen receptor signaling. Sci. Signal. Available: http://stke.sciencemag.org/cgi/cm/stkecm;CMP_6906. Accessed 2009 Sep 10.
36. Mishra L, Kitisin K, Saha T, Blake T, Golestaneh N, et al. TGF-beta signaling in development. Sci. Signal. Available: http://stke.sciencemag.org/cgi/cm/stkecm;CMP_18196. Accessed 2009 Sep 10.
37. Horvath CM, Aaronson DS. Interferon gamma pathway. Sci. Signal. Available: http://stke.sciencemag.org/cgi/cm/stkecm;CMP_9590. Accessed 2009 Sep 10.
38. Gough NR (2002) Science's signal transduction knowledge environment: the connections maps database. Ann N Y Acad Sci 971: 585-587.
39. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827.
40. Gomperts BD, Kramer IM, Tatham PER (2002) Signal transduction. Academic Press.
41. Kirschner M, Gerhart J (1998) Evolvability. PNAS 95: 8420-8427.
42. Wagner A (2005) Robustness and evolvability in living systems. Princeton University Press.
43. Shinar G, Milo R, Martínez MR, Alon U (2007) Input output robustness in simple bacterial signaling systems. Proc Natl Acad Sci U S A 104: 19931-19935.
44. Wagner A, Wright J (2004) Compactness and cycles in signal transduction and transcriptional regulation networks: a signature of natural selection? Advances in Complex Systems 7: 419-432.