Biological role of noise encoded in a genetic network motif

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 30, 2010, Pages 13300-13305

  Kittisopikul, Mark ^a   Süel, Gürol M ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Demand theory; Design principles; Gene expression bursts; Shot noise; Stochastic simulation

Indexed keywords

ARTICLE; CELL ACTIVITY; COMPUTATIONAL FLUID DYNAMICS; CONTROLLED STUDY; ENVIRONMENTAL STRESS; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; NOISE; NONHUMAN; PRIORITY JOURNAL; STEADY STATE; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; PHYSIOLOGY; PROCEDURES; PROTEIN MOTIF; PROTEIN SYNTHESIS; STATISTICS;

ESCHERICHIA COLI PROTEIN;

AMINO ACID MOTIFS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; SOFTWARE; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 77955830290     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1003975107     Document Type: Article

References (51)

1. Tsai TY-C, et al. (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321:126-129.
2. Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100:11980-11985. (Pubitemid 37271501)
3. Kollmann M, Løvdok L, Bartholomé K, Timmer J, Sourjik V (2005) Design principles of a bacterial signalling network. Nature 438(7067):504-507. (Pubitemid 41742022)
4. Alon U (2007) Network motifs: Theory and experimental approaches. Nat Rev Genet 8 (6):450-461.
5. Stricker J, et al. (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516-519. (Pubitemid 352759003)
6. Choi PJ, Cai L, Frieda K, Xie XS (2008) A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322(5900):442-446.
7. Cagatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Süel GM (2009) Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139(3):512-522.
8. Igoshin OA, Brody MS, Price CW, Savageau MA (2007) Distinctive topologies of partner-switching signaling networks correlate with their physiological roles. J Mol Biol 369(5):1333-1352.
9. Klemm K, Bornholdt S (2005) Topology of biological networks and reliability of information processing. Proc Natl Acad Sci USA 102:18414-18419. (Pubitemid 43011240)
10. Wall ME, Hlavacek WS, Savageau MA (2003) Design principles for regulator gene expression in a repressible gene circuit. J Mol Biol 332(4):861-876.
11. Savageau MA (2001) Design principles for elementary gene circuits: Elements, methods, and examples. Chaos 11(1):142-159. (Pubitemid 33245069)
12. Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440(7083):545-550.
13. Süel GM, Kulkarni RP, Dworkin J, Garcia-Ojalvo J, Elowitz MB (2007) Tunability and noise dependence in differentiation dynamics. Science 315(5819):1716-1719. (Pubitemid 46515626)
14. Milo R, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298(5594):824-827. (Pubitemid 35231534)
15. Kim HD, Shay T, O'Shea EK, Regev A (2009) Transcriptional regulatory circuits: predicting numbers from alphabets. Science 325(5939):429-432.
16. Alon U (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC, Boca Raton), (in English), p 301.
17. Mangan S, Itzkovitz S, Zaslaver A, Alon U (2006) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356(5):1073-1081. (Pubitemid 43199913)
18. Turcotte M, Garcia-Ojalvo J, Süel GM (2008) A genetic timer through noise-induced stabilization of an unstable state. Proc Natl Acad Sci USA 105:15732-15737.
19. Hornos JE, et al. (2005) Self-regulating gene: an exact solution. Phys Rev E 72:051907.
20. Schultz D, Onuchic JN,Wolynes PG (2007) Understanding stochastic simulations of the smallest genetic networks. J Chem Phys 126(24):245102.
21. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A (2002) Regulation of noise in the expression of a single gene. Nat Genet 31(1):69-73.
22. Yu J, Xiao J, Ren X, Lao K, Xie XS (2006) Probing gene expression in live cells, one protein molecule at a time. Science 311(5767):1600-1603.
23. Ingram PJ, Stumpf MPH, Stark J (2008) Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data. PLoS Comput Biol 4(10):e1000192.
24. Maamar H, Raj A, Dubnau D (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317(5837):526-529. (Pubitemid 47196119)
25. Schultz D, Ben Jacob E, Onuchic JN, Wolynes PG (2007) Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc Natl Acad Sci USA 104:17582-17587. (Pubitemid 350210878)
26. Shahrezaei V, Ollivier JF, Swain PS (2008) Colored extrinsic fluctuations and stochastic gene expression. Mol Syst Biol 4:196. (Pubitemid 351655226)
27. Dunlop MJ, Cox RS, Levine JH, Murray RM, Elowitz MB (2008) Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet 40(12):1493-1498.
28. Ghosh B, Karmakar R, Bose I (2005) Noise characteristics of feed forward loops. Phys Biol 2(1):36-45. (Pubitemid 41238216)
29. Hansen S, Lewis K, Vulić M (2008) Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli. Antimicrob Agents Chemother 52(8): 2718-2726.
30. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem US 81(25):2340-2361.
31. Gillespie DT (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58:35-55.
32. Keseler IM, et al. (2009) EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res 37:D464-D470 (database issue).
33. Gama-Castro S, et al. (2008) RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36:D120-D124 (database issue).
34. Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187(3):1135-1160. (Pubitemid 40189786)
35. Freed NE, et al. (2008) A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genet 4(12):e1000307.
36. Cai L, Dalal CK, Elowitz MB (2008) Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455(7212):485-490.
37. Leon J, Garcia-Lobo JM, Ortiz JM (1982) Fosfomycin resistance plasmids do not affect fosfomycin transport into Escherichia coli. Antimicrob Agents Chemother 21(4):608-612. (Pubitemid 12070531)
38. Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastics witching as a survival strategy in fluctuating environments. Nat Genet 40(4):471-475. (Pubitemid 351450880)
39. Wolf DM, Vazirani VV, Arkin AP (2005) Diversity in times of adversity: Probabilistic strategies in microbial survival games. J Theor Biol 234(2):227-253.
40. Thattai M, van Oudenaarden A (2004) Stochastic gene expression in fluctuating environments. Genetics 167(1):523-530. (Pubitemid 38736407)
41. Savageau MA (1998) Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. Genetics 149(4):1677-1691.
42. Savageau MA (1998) Demand theory of gene regulation. I. Quantitative development of the theory. Genetics 149(4):1665-1676.
43. Golding I, Paulsson J, Zawilski SM, Cox EC (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123(6):1025-1036. (Pubitemid 41785418)
44. Wang Y, Guo L, Golding I, Cox EC, Ong NP (2009) Quantitative transcription factor binding kinetics at the single-molecule level. Biophys J 96(2):609-620.
45. Leisner M, Kuhr J-T, Rädler JO, Frey E, Maier B (2009) Kinetics of genetic switching into the state of bacterial competence. Biophys J 96(3):1178-1188.
46. Leisner M, Stingl K, Frey E, Maier B (2008) Stochastic switching to competence. Curr Opin Microbiol 11(6):553-559.
47. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science 305(5690):1622-1625.
48. Pineda-Krch M (2008) GillespieSSA: Implementing the stochastic simulation algorithm in R. J Stat Softw 25(12):1-18.
49. Wernicke S, Rasche F (2006) FANMOD: A tool for fast network motif detection. Bioinformatics 22(9):1152-1153.
50. Ma H-W, Buer J, Zeng A-P (2004) Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics 5:199. (Pubitemid 40195310)
51. Davidson AC, Hinkley DV (1997) Bootstrap Methods and Their Applications (Cambridge Univ Press, Cambridge).