Engineering stochasticity in gene expression

Molecular BioSystems

Volumn 4, Issue 7, 2008, Pages 754-761

  Tabor, Jeffrey J ^a,c   Bayer, Travis S ^b   Simpson, Zachary B ^a   Levy, Matthew ^a   Ellington, Andrew D ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; BIOLOGICAL MODEL; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC ENGINEERING; GENETICS; METABOLISM; OPERON; PHENOTYPE; RIBOSOME; STATISTICS;

ESCHERICHIA COLI; GENE EXPRESSION; GENETIC ENGINEERING; MODELS, BIOLOGICAL; OPERON; PHENOTYPE; RIBOSOMES; RNA; STOCHASTIC PROCESSES;

EID: 45849128019     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/b801245h     Document Type: Article

References (57)

1. H. H. McAdams A. Arkin Stochastic mechanisms in gene expression Proc. Natl. Acad. Sci. U. S. A. 1997 94 814 9
2. A. Becskei B. B. Kaufmann A. van Oudenaarden Contributions of low molecule number and chromosomal positioning to stochastic gene expression Nat. Genet. 2005 37 937 44
3. W. J. Blake K. A. M C. R. Cantor J. J. Collins Noise in eukaryotic gene expression Nature 2003 422 633 7
4. I. Golding J. Paulsson S. M. Zawilski E. C. Cox Real-time kinetics of gene activity in individual bacteria Cell 2005 123 1025 36
5. J. M. Raser E. K. O'Shea Control of stochasticity in eukaryotic gene expression Science 2004 304 1811 4
6. W. J. Blake G. Balazsi M. A. Kohanski F. J. Isaacs K. F. Murphy Y. Kuang C. R. Cantor D. R. Walt J. J. Collins Phenotypic consequences of promoter-mediated transcriptional noise Mol. Cell 2006 24 853 65
7. J. M. Pedraza J. Paulsson Effects of molecular memory and bursting on fluctuations in gene expression Science 2008 319 339 43
8. A. Bar-Even J. Paulsson N. Maheshri M. Carmi E. O'Shea Y. Pilpel N. Barkai Noise in protein expression scales with natural protein abundance Nat. Genet. 2006 38 636 43
9. J. R. Newman S. Ghaemmaghami J. Ihmels D. K. Breslow M. Noble J. L. Derisi J. S. Weissman Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise Nature 2006
10. J. Paulsson Summing up the noise in gene networks Nature 2004 427 415 8
11. P. S. Swain Efficient attenuation of stochasticity in gene expression through post-transcriptional control J. Mol. Biol. 2004 344 965 76
12. L. Cai N. Friedman X. S. Xie Stochastic protein expression in individual cells at the single molecule level Nature 2006 440 358 62
13. J. Yu J. Xiao X. Ren K. Lao X. S. Xie Probing gene expression in live cells, one protein molecule at a time Science 2006 311 1600 3
14. E. M. Ozbudak M. Thattai I. Kurtser A. D. Grossman A. van Oudenaarden Regulation of noise in the expression of a single gene Nat. Genet. 2002 31 69 73
15. M. Thattai A. van Oudenaarden Intrinsic noise in gene regulatory networks Proc. Natl. Acad. Sci. U. S. A. 2001 98 8614 9
16. U. N. Singh Polyribosomes and unstable messenger RNA: a stochastic model of protein synthesis J. Theor. Biol. 1969 25 444 60
17. M. B. Elowitz A. J. Levine E. D. Siggia P. S. Swain Stochastic gene expression in a single cell Science 2002 297 1183 6
18. J. M. Pedraza A. van Oudenaarden Noise propagation in gene networks Science 2005 307 1965 9
19. D. Volfson J. Marciniak W. J. Blake N. Ostroff L. S. Tsimring J. Hasty Origins of extrinsic variability in eukaryotic gene expression Nature 2005
20. N. J. Guido P. Lee X. Wang T. C. Elston J. J. Collins A pathway and genetic factors contributing to elevated gene expression noise in stationary phase Biophys. J. 2007
21. A. Colman-Lerner A. Gordon E. Serra T. Chin O. Resnekov D. Endy C. G. Pesce R. Brent Regulated cell-to-cell variation in a cell-fate decision system Nature 2005 437 699 706
22. N. Rosenfeld J. W. Young U. Alon P. S. Swain M. B. Elowitz Gene regulation at the single-cell level Science 2005 307 1962 5
23. J. R. Chabot J. M. Pedraza P. Luitel A. van Oudenaarden Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock Nature 2007 450 1249 52
24. D. A. Drubin J. C. Way P. A. Silver Designing biological systems Genes Dev. 2007 21 242 54
25. D. Sprinzak M. B. Elowitz Reconstruction of genetic circuits Nature 2005 438 443 8
26. B. J. Yeh W. A. Lim Synthetic biology: lessons from the history of synthetic organic chemistry Nat. Chem. Biol. 2007 3 521 5
27. N. J. Guido X. Wang D. Adalsteinsson D. McMillen J. Hasty C. R. Cantor T. C. Elston J. J. Collins A bottom-up approach to gene regulation Nature 2006 439 856 60
28. T. S. Gardner C. R. Cantor J. J. Collins Construction of a genetic toggle switch in Escherichia coli Nature 2000 403 339 42
29. M. B. Elowitz S. Leibler A synthetic oscillatory network of transcriptional regulators Nature 2000 403 335 8
30. G. M. Suel R. P. Kulkarni J. Dworkin J. Garcia-Ojalvo M. B. Elowitz Tunability and noise dependence in differentiation dynamics Science 2007 315 1716 9
31. G. M. Suel J. Garcia-Ojalvo L. M. Liberman M. B. Elowitz An excitable gene regulatory circuit induces transient cellular differentiation Nature 2006 440 545 50
32. L. S. Weinberger J. C. Burnett J. E. Toettcher A. P. Arkin D. V. Schaffer Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity Cell 2005 122 169 82
33. F. J. Isaacs D. J. Dwyer C. Ding D. D. Pervouchine C. R. Cantor J. J. Collins Engineered riboregulators enable post-transcriptional control of gene expression Nat. Biotechnol. 2004 22 841 7
34. E. Masse S. Gottesman A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli Proc. Natl. Acad. Sci. U. S. A. 2002 99 4620 5
35. T. Moller T. Franch C. Udesen K. Gerdes P. Valentin-Hansen Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon Genes Dev. 2002 16 1696 706
36. W. Winkler A. Nahvi R. R. Breaker Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 2002 419 952 6
37. G. A. Soukup R. R. Breaker Relationship between internucleotide linkage geometry and the stability of RNA RNA 1999 5 1308 25
38. S. T. Liang Y. C. Xu P. Dennis H. Bremer mRNA composition and control of bacterial gene expression J. Bacteriol. 2000 182 3037 44
39. B. Xia J. P. Etchegaray M. Inouye Nonsense mutations in cspA cause ribosome trapping leading to complete growth inhibition and cell death at low temperature in Escherichia coli J. Biol. Chem. 2001 276 35581 8
40. J. R. Newman S. Ghaemmaghami J. Ihmels D. K. Breslow M. Noble J. L. DeRisi J. S. Weissman Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise Nature 2006 441 840 6
41. P. Regnier C. M. Arraiano Degradation of mRNA in bacteria: emergence of ubiquitous features Bioessays 2000 22 235 44
42. A. Arkin J. Ross H. H. McAdams Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells Genetics 1998 149 1633 48
43. A. D. Grossman Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis Annu. Rev. Genet. 1995 29 477 508
44. R. Kemkemer S. Schrank W. Vogel H. Gruler D. Kaufmann Increased noise as an effect of haploinsufficiency of the tumor-suppressor gene neurofibromatosis type 1 in vitro Proc. Natl. Acad. Sci. U. S. A. 2002 99 13783 8
45. H. Maughan W. L. Nicholson Stochastic processes influence stationary-phase decisions in Bacillus subtilis J. Bacteriol. 2004 186 2212 4
46. D. M. Wolf V. V. Vazirani A. P. Arkin Diversity in times of adversity: probabilistic strategies in microbial survival games J. Theor. Biol. 2005 234 227 53
47. A. M. Giuliodori A. Brandi C. O. Gualerzi C. L. Pon Preferential translation of cold-shock mRNAs during cold adaptation RNA 2004 10 265 276
48. F. Fiedler G. V. Mallo H. Bodeker V. Keim J. C. Dagorn J. L. Iovanna Overexpression of the PC3/TIS21/BTG2 mRNA is part of the stress response induced by acute pancreatitis in rats Biochem. Biophys. Res. Commun. 1998 249 562 5
49. A. Brandi R. Spurio C. O. Gualerzi C. L. Pon Massive presence of the Escherichia coli 'major cold-shock protein' CspA under non-stress conditions EMBO J. 1999 18 1653 9
50. K. Yamanaka M. Inouye Induction of CspA, an E. coli major cold-shock protein, upon nutritional upshift at 37 degrees C Genes Cells 2001 6 279 90
51. W. J. Welch H. S. Kang R. P. Beckmann L. A. Mizzen Response of mammalian cells to metabolic stress; changes in cell physiology and structure/function of stress proteins Curr. Top. Microbiol. Immunol. 1991 167 31 55
52. L. Y. Wei P. D. Roepe Low external pH and osmotic shock increase the expression of human MDR protein Biochemistry 1994 33 7229 38
53. P. G. Jones R. A. VanBogelen F. C. Neidhardt Induction of proteins in response to low temperature in Escherichia coli J. Bacteriol. 1987 169 2092 5
54. D. A. Colon-Ramos C. L. Shenvi D. H. Weitzel E. C. Gan R. Matts J. Cate S. Kornbluth Direct ribosomal binding by a cellular inhibitor of translation Nat. Struct. Mol. Biol. 2006 13 103 111
55. J. G. Lawrence Shared strategies in gene organization among prokaryotes and eukaryotes Cell 2002 110 407 13
56. T. Dandekar B. Snel M. Huynen P. Bork Conservation of gene order: a fingerprint of proteins that physically interact Trends Biochem. Sci. 1998 23 324 8
57. D. K. Ro E. M. Paradise M. Ouellet K. J. Fisher K. L. Newman J. M. Ndungu K. A. Ho R. A. Eachus T. S. Ham J. Kirby M. C. Chang S. T. Withers Y. Shiba R. Sarpong J. D. Keasling Production of the antimalarial drug precursor artemisinic acid in engineered yeast Nature 2006 440 940 3