Recurrent design patterns in the feedback regulation of the mammalian signalling network

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  Legewie, Stefan ^a   Herzel, Hanspeter ^a   Westerhoff, Hans V ^b,c,d   Blüthgen, Nils ^c  

^a HUMBOLDT UNIVERSITY   (Germany)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Evolutionary trade off; Gene regulation; Protein turnover; Signal transduction

Indexed keywords

ARTICLE; FEEDBACK SYSTEM; GENE CONTROL; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; KINETICS; MAMMAL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROTEIN METABOLISM; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; ANIMAL; GENE EXPRESSION REGULATION; GENETICS; HALF LIFE TIME; METABOLISM;

MAMMALIA;

MESSENGER RNA;

ANIMALS; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION; HALF-LIFE; KINETICS; MAMMALS; RNA, MESSENGER; SIGNAL TRANSDUCTION;

EID: 43249098417     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2008.29     Document Type: Article

References (22)

1. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461
2. Altan-Bonnet G, Germain RN (2005) Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biol 3: e356
3. Amit I, Citri A, Shay T, Lu Y, KatzM, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E, Yarden Y (2007) A module of negative feedback regulators defines growth factor signaling. Nat Genet 39: 503-512
4. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, FujibuchiW, Edgar R (2005) NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 33 (Database issue): D562-D566
5. Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK (2006) Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci USA 103: 13004-13009
6. Bluthgen N, Menzel F, Hovestadt T, Fiala B, Bluthgen N (2007) Specialization, constraints, and conflicting interests in mutualistic networks. Curr Biol 17: 341-346
7. Dublanche Y, Michalodimitrakis K, Kummerer N, Foglierini M, Serrano L (2006)Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol 2: 41
8. Heinrich R, Neel BG, Rapoport TA (2002) Mathematical models of protein kinase signal transduction. Mol Cell 9: 957-970
9. Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, de Vaate AJ, Lankelma J, Heinrich R, Westerhoff HV (2005) Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. FEBS J 272: 244-258
10. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL (2000) The largescale organization of metabolic networks. Nature 407: 651-654
11. Kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V (2005) Design principles of a bacterial signalling network. Nature 438: 504-507
12. Martin H, Flandez M, Nombela C, Molina M (2005) Protein phosphatases in MAPK signalling: we keep learning from yeast. Mol Microbiol 58: 6-16
13. Mettetal JT, Muzzey D, Gomez-Uribe C, van Oudenaarden A (2008) The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science 319: 482-484
14. Nissen R, Cardinale GJ, Udenfriend S (1978) Increased turnover of arterial collagen in hypertensive rats. Proc Natl Acad Sci USA 75: 451-453
15. Raghavan A, Ogilvie RL, Reilly C, AbelsonML, Raghavan S, Vasdewani J, Krathwohl M, Bohjanen PR (2002) Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res 30: 5529-5538
16. Rao CV, Wolf DM, Arkin AP (2002) Control, exploitation and tolerance of intracellular noise. Nature 420: 231-237
17. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880
18. Santos SD, Verveer PJ, Bastiaens PI (2007) Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat Cell Biol 9: 324-330
19. Sauro HM, Kholodenko BN (2004) Quantitative analysis of signaling networks. Prog Biophys Mol Biol 86: 5-43
20. Wang E, Purisima E (2005) Network motifs are enriched with transcription factors whose transcripts have short half-lives. Trends Genet 21: 492-495
21. Wieser W, Krumschnabel G (2001) Hierarchies of ATP-consuming processes: direct compared with indirect measurements, and comparative aspects. Biochem J 355: 389-395
22. Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell Jr JE (2003) Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res 13: 1863-1872