Translational Cross Talk in Gene Networks

Biophysical Journal

Volumn 104, Issue 11, 2013, Pages 2564-2572

  Mather, William H ^a   Hasty, Jeff ^b,c,d,e   Tsimring, Lev S ^b,d   Williams, Ruth J ^b,d  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e University of California San Diego   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; BIOLOGICAL MODEL; GENE REGULATORY NETWORK; GENETICS; PROTEIN SYNTHESIS; RIBOSOME; STATISTICS;

GENE REGULATORY NETWORKS; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER; STOCHASTIC PROCESSES;

EID: 84878866199     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.04.049     Document Type: Article

References (47)

1. H. Lodish, and A. Berk M.P. Scott Molecular Cell Biology 7th ed. 2012 W. H. Freeman New York
2. I.L. Grigorova, and N.J. Phleger C.A. Gross Insights into transcriptional regulation and σ competition from an equilibrium model of RNA polymerase binding to DNA Proc. Natl. Acad. Sci. USA 103 2006 5332 5337
3. S. Klumpp, and T. Hwa Growth-rate-dependent partitioning of RNA polymerases in bacteria Proc. Natl. Acad. Sci. USA 105 2008 20245 20250
4. C.A. Voigt Genetic parts to program bacteria Curr. Opin. Biotechnol. 17 2006 548 557
5. P.E.M. Purnick, and R. Weiss The second wave of synthetic biology: from modules to systems Nat. Rev. Mol. Cell Biol. 10 2009 410 422
6. G. Alterovitz, T. Muso, and M.F. Ramoni The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms Brief. Bioinform. 11 2010 80 95
7. T.S. Lee, and R.A. Krupa J.D. Keasling BglBrick vectors and datasheets: a synthetic biology platform for gene expression J Biol Eng 5 2011 12
8. K.J. Morey, and M.S. Antunes J. Medford Crosstalk between endogenous and synthetic components - synthetic signaling meets endogenous components Biotechnol. J. 7 2012 846 855
9. A.A. Cheng, and T.K. Lu Synthetic biology: an emerging engineering discipline Annu. Rev. Biomed. Eng. 14 2012 155 178
10. A.L. Slusarczyk, A. Lin, and R. Weiss Foundations for the design and implementation of synthetic genetic circuits Nat. Rev. Genet. 13 2012 406 420
11. D. Del Vecchio, A.J. Ninfa, and E.D. Sontag Modular cell biology: retroactivity and insulation Mol. Syst. Biol. 4 2008 161
12. K.H. Kim, and H.M. Sauro Fan-out in gene regulatory networks J. Biol. Eng. 4 2010 16
13. N.A. Cookson, and W.H. Mather J. Hasty Queueing up for enzymatic processing: correlated signaling through coupled degradation Mol. Syst. Biol. 7 2011 561
14. K.H. Kim, and H.M. Sauro Measuring retroactivity from noise in gene regulatory networks Biophys. J. 100 2011 1167 1177
15. Y. Rondelez Competition for catalytic resources alters biological network dynamics Phys. Rev. Lett. 108 2012 018102
16. N.E. Buchler, and M. Louis Molecular titration and ultrasensitivity in regulatory networks J. Mol. Biol. 384 2008 1106 1119
17. S.A. Chapman, and A.R. Asthagiri Quantitative effect of scaffold abundance on signal propagation Mol. Syst. Biol. 5 2009 313
18. A.J. Genot, T. Fujii, and Y. Rondelez Computing with competition in biochemical networks Phys. Rev. Lett. 109 2012 208102
19. J.R. Warner, J. Vilardell, and J.H. Sohn Economics of ribosome biosynthesis Cold Spring Harb. Symp. Quant. Biol. 66 2001 567 574
20. V.P. Mauro, and G.M. Edelman The ribosome filter hypothesis Proc. Natl. Acad. Sci. USA 99 2002 12031 12036
21. V.P. Mauro, and G.M. Edelman The ribosome filter redux Cell Cycle 6 2007 2246 2251
22. I. Shachrai, and A. Zaslaver E. Dekel Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth Mol. Cell 38 2010 758 767 10.1016/j.molcel.2010.04.015
23. M. Scott, and C.W. Gunderson T. Hwa Interdependence of cell growth and gene expression: origins and consequences Science 330 2010 1099 1102
24. D. De Vos, and F.J. Bruggeman B.M. Bakker How molecular competition influences fluxes in gene expression networks PLoS ONE 6 2011 e28494
25. D. Chu, D.J. Barnes, and T. von der Haar The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae Nucleic Acids Res. 39 2011 6705 6714
26. M.R. Bennett, and W.L. Pang J. Hasty Metabolic gene regulation in a dynamically changing environment Nature 454 2008 1119 1122
27. B.L. Baumgartner, and M.R. Bennett J. Hasty Antagonistic gene transcripts regulate adaptation to new growth environments Proc. Natl. Acad. Sci. USA 108 2011 21087 21092
28. S. Asmussen Applied Probability and Queues 2nd ed. 2003 Springer-Verlag New York
29. A. Arazi, E. Ben-Jacob, and U. Yechiali Bridging genetic networks and queueing theory Physica A 332 2004 585 616
30. E. Levine, and T. Hwa Stochastic fluctuations in metabolic pathways Proc. Natl. Acad. Sci. USA 104 2007 9224 9229
31. A. Fredriksson, and M. Ballesteros T. Nyström Decline in ribosomal fidelity contributes to the accumulation and stabilization of the master stress response regulator σS upon carbon starvation Genes Dev. 21 2007 862 874
32. V. Elgart, T. Jia, and R.V. Kulkarni Applications of Little's Law to stochastic models of gene expression Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 82 2010 021901
33. W.H. Mather, and N.A. Cookson R.J. Williams Correlation resonance generated by coupled enzymatic processing Biophys. J. 99 2010 3172 3181
34. W.H. Mather, and J. Hasty R.J. Williams Factorized time-dependent distributions for certain multiclass queueing networks and an application to enzymatic processing networks Queueing Syst. 69 2011 313 328
35. T. Jia, and R.V. Kulkarni Intrinsic noise in stochastic models of gene expression with molecular memory and bursting Phys. Rev. Lett. 106 2011 058102
36. F.P. Kelly Effective bandwidths at multi-class queues Queueing Syst. 9 1991 5 15
37. L. Rajkowitsch, and C. Vilela J.E. McCarthy Reinitiation and recycling are distinct processes occurring downstream of translation termination in yeast J. Mol. Biol. 335 2004 71 85
38. C. Gadgil, C.H. Lee, and H.G. Othmer A stochastic analysis of first-order reaction networks Bull. Math. Biol. 67 2005 901 946
39. J.M. Raser, and E.K. O'Shea Control of stochasticity in eukaryotic gene expression Science 304 2004 1811 1814
40. Y. Taniguchi, and P.J. Choi X.S. Xie Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329 2010 533 538
41. B. Munsky, G. Neuert, and A. van Oudenaarden Using gene expression noise to understand gene regulation Science 336 2012 183 187
42. F. Gebauer, and M.W. Hentze Molecular mechanisms of translational control Nat. Rev. Mol. Cell Biol. 5 2004 827 835
43. S.P. Gygi, and Y. Rochon R. Aebersold Correlation between protein and mRNA abundance in yeast Mol. Cell. Biol. 19 1999 1720 1730
44. Y. Guo, and P. Xiao H. Deng How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes Acta Biochim. Biophys. Sin. (Shanghai) 40 2008 426 436
45. D. Greenbaum, and C. Colangelo M. Gerstein Comparing protein abundance and mRNA expression levels on a genomic scale Genome Biol. 4 2003 117
46. D.H. Lackner, and M.W. Schmidt J. Bähler Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast Genome Biol. 13 2012 R25
47. C. Gardiner Stochastic Methods: A Handbook for the Natural and Social Sciences 2009 Springer Berlin