How molecular competition influences fluxes in gene expression networks

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  de Vos, Dirk ^a,b,f   Bruggeman, Frank J ^a,c   Westerhoff, Hans V ^a,b,d   Bakker, Barbara M ^a,b,e  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

^c CWI   (Netherlands)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

^e UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^f UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; SIGMA FACTOR;

ARTICLE; BACTERIAL GENE; BINDING COMPETITION; FUNGAL GENOME; GENE EXPRESSION; GENETIC TRANSCRIPTION; MOLECULAR INTERACTION; RIBOSOME; THEORETICAL STUDY; YEAST; ALGORITHM; BIOLOGICAL MODEL; ESCHERICHIA COLI; FUNGAL GENE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN SYNTHESIS; STATISTICAL MODEL;

ALGORITHMS; ESCHERICHIA COLI; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENES, FUNGAL; GENOME, FUNGAL; MODELS, GENETIC; MODELS, STATISTICAL; PROTEIN BIOSYNTHESIS; RNA, MESSENGER; SIGMA FACTOR; TRANSCRIPTION, GENETIC;

EID: 82655179954     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028494     Document Type: Article

References (55)

1. Tyson JJ, Chen KC, Novak B, (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221-231.
2. Alon U, (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
3. Maaloe O, (1979) Regulation of the protein synthesizing machinery - ribosomes, tRNA, factors and so on. In: Goldberger RF, editors. Biological regulation and development New York Plenum Publishing Corp pp. 487-542.
4. Warner J, (1999) The economics of ribosome biosynthesis in yeast. TIBS 24: 437-440.
5. Lovmar M, Ehrenberg M, (2006) Rate, accuracy and cost of ribosomes in bacterial cells. Biochimie 88: 951-961.
6. Mehra A, Hatzimanikatis V, (2006) An algorithmic framework for genome-wide modeling and analysis of translation networks. Biophys J 90: 1136-1146.
7. Mooney RA, Darst SA, Landick R, (2005) Sigma and RNA polymerase: an on-again, off-again relationship. Mol Cell 20: 335-345.
8. Nystrom T, (2004) Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 54: 855-862.
9. Dong T, Yu R, Schellhorn H, (2011) Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli. Mol Microbiol 79: 375-386.
10. Maeda H, Fujita N, Ishihama A, (2000) Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res 28: 3497-3503.
11. Merrick MJ, (1993) In a class of its own - the RNA polymerase sigma factor sigma 54 (sigma N). Mol Microbiol 10: 903-909.
12. Shingler V, (1996) Signal sensing by sigma 54-dependent regulators: derepression as a control mechanism. Mol Microbiol 19: 400-416.
13. Helmann JD, (1991) Alternative sigma factors and the regulation of flagellar gene expression. Mol Microbiol 5: 2875-2882.
14. Ishihama A, (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54: 499-518.
15. Kacser H, Burns JA, (1973) The control of flux. Symp Soc Exp Biol 27: 65-104.
16. Heinrich R, Rapoport TA, (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Bioch 42: 89-95.
17. Reder C, (1988) Metabolic control theory: a structural approach. J Theor Biol 135: 175-201.
18. Goldbeter A, Koshland DE Jr, (1982) Sensitivity amplification in biochemical systems. Q Rev Biophys 15: 555-591.
19. Hofmeyr JHS, Kacser H, van der Merwe KJ, (1986) Metabolic control analysis of moiety-conserved cycles. Eur J Biochem 155: 631-641.
20. Sauro HM, (1994) Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channeling. BioSystems 33: 55-67.
21. Kholodenko BN, Sauro HM, Westerhoff HV, (1994) Control by enzymes, coenzymes and conserved moieties. A generalization of the connectivity theorem of metabolic control analysis. Eur J Biochem 225: 179-186.
22. Goldbeter A, Koshland DE Jr, (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A 78: 6840-6844.
23. Heinrich R, Rapoport TA, (1980) Mathematical modeling of translation of messenger-RNA in eukaryotes - steady-states, time-dependent processes and application to reticulocytes. J Theor Biol 86: 279-313.
24. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889-3894.
25. Mackay VL, Li X, Flory MR, Turcott E, Law GL, et al. (2004) Gene expression analyzed by high-resolution state array analysis and quantitative proteomics. Mol Cell Proteomics 3: 478-489.
26. Siwiak M, Zielenkiewicz P, (2010) A comprehensive, quantitative, and genome-wide model of translation. PLoS Comp Biol: 6: e1000865.
27. Brockmann R, Beyer A, Heinisch JJ, Wilhelm T, (2007) Posttranscriptional expression regulation: what determines translation rates? PLoS Comp Biol: 3: e57.
28. Fell D, (1997) Understanding the Control of Metabolism. London Portland Press.
29. LaPorte DC, Walsh K, Koshland DE, Jr, (1984) The branch point effect. J Biol Chem 259: 14068-14075.
30. Blüthgen N, Bruggeman FJ, Legewie S, Herzel H, Westerhoff HV, et al. (2006) Effects of sequestration on signal transduction cascades. FEBS J 273: 895-906.
31. Kim SY, Ferrell JE Jr, (2007) Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell 128: 1133-1145.
32. Liu X, Matsumura P, (1996) Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli. Mol Microbiol 21: 613-620.
33. Farewell A, Kvint K, Nystrom T, (1998) Negative regulation by RpoS: a case of sigma factor competition. Mol Microbiol 29: 1039-1052.
34. Notley-McRobb L, King T, Ferenci T, (2002) rpoS mutations and loss of general stress resistance in Escherichia coli populations as a consequence of conflict between competing stress responses. J Bacteriol 184: 806-811.
35. Jishage M, Kvint K, Shingler V, Nystrom T, (2002) Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev 16: 1260-1270.
36. Malik S, Zalenskaya K, Goldfarb A, (1987) Competition between sigma factors for core RNA polymerase. Nucleic Acids Res 15: 8521-8530.
37. Jishage M, Iwata A, Ueda S, Ishihama A, (1996) Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions. J Bacteriol 178: 5447-5451.
38. Kawakami K, Saitoh T, Ishihama A, (1979) Biosynthesis of RNA polymerase in Escherichia coli, ix. growth-dependent variations in the synthesis rate, content and distribution of RNA polymerase. Mol Gen Genetics 174: 107-116.
39. Makinoshima H, Aizawa S, Hayashi H, Miki T, Nishimura A, Ishihama A, (2003) Growth phase-coupled alterations in cell structure and function of Escherichia coli. J Bacteriol 185: 1338-1345.
40. Dong T, Schellhorn HE, (2009a) Control of RpoS in global gene expression of Escherichia coli in minimal media. Mol Genet Genomics 281: 19-33.
41. Zambrano MM, Siegele DA, Almiron M, Tormo A, Kolter R, (1993) Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259: 1757-1760.
42. Krogfelt KA, Hjulgaard M, Sorensen K, Cohen PS, Givskov M, (2000) rpoS gene function is a disadvantage for Escherichia coli BJ4 during competitive colonization of the mouse large intestine. Infect Immun 68: 2518-2524.
43. Dong T, Schellhorn HE, (2009b) Global effect of RpoS on gene expression in pathogenic Escherichia coli O157: H7 strain EDL933. BMC Genomics 10: 349.
44. Jensen K, Pedersen S, (1990) Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components. Microbiol Rev 54: 89-100.
45. Dennis PP, Ehrenberg M, Bremer H, (2004) Control of rRNA synthesis in Escherichia coli: a systems biology approach. Micr Mol Biol Rev 68: 639-668.
46. Kjeldgaard NO, Kurland CG, (1963) The distribution of soluble and ribosomal RNA as a function of growth rate. J Mol Biol 6: 341-348.
47. Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn MM, Pronk JT, et al. (2006) Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol 2: 2006.0026.
48. Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, et al. (2007) The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci U S A 104: 15753-15758.
49. Dobrzynski M, Bruggeman FJ, (2009) Elongation dynamics shape bursty transcription and translation. Proc Natl Acad Sci U S A 106: 2583-2588.
50. Schwabe A, Dobrzyński M, Rybakova K, Verschure P, Bruggeman FJ, (2011) Origins of stochastic intracellular processes and consequences for cell-to-cell variability and cellular survival strategies. Methods Enzymol 500: 597-625.
51. Mitchell P, Tollervey D, (2001) mRNA turnover. Curr Opin Cell Biol 13: 320-325.
52. Dantuma NP, Groothuis TA, Salomons FA, Neefjes J, (2006) A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling. J Cell Biol 173: 19-26.
53. Moore MJ, Proudfoot NJ, (2009) Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136: 688-700.
54. Kazazian HH, Freedman ML, (1968) The characterization of separated alpha- and beta-chain polyribosomes in rabbit reticulocytes. J Biol Chem 243: 6446-6450.
55. Rose JK, (1977) Nucleotide sequences of ribosome recognition sites in messenger RNAs of vesicular stomatitis virus. Proc Natl Acad Sci USA 74: 3672-3676.