Single-molecule dynamics of transcription of the lar promoter

Physical Biology

Volumn 9, Issue 2, 2012, Pages

  Kandhavelu, M ^a   Hakkinen A ^a   Yli Harja, O ^a,b   Ribeiro, A S ^a  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

BACTERIAL RNA; GREEN FLUORESCENT PROTEIN;

ARTICLE; COLIPHAGE; CONFOCAL MICROSCOPY; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; GENETICS; KINETICS; LACTOSE OPERON; METABOLISM; POISSON DISTRIBUTION; PROMOTER REGION; TIME; TRANSCRIPTION INITIATION;

ESCHERICHIA COLI; GREEN FLUORESCENT PROTEINS; KINETICS; LAC OPERON; LEVIVIRUS; MICROSCOPY, CONFOCAL; POISSON DISTRIBUTION; PROMOTER REGIONS, GENETIC; RNA, BACTERIAL; TIME FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 84859593811     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/9/2/026004     Document Type: Article

References (37)

1. Fusco D, Accornero N, Lavoie B, Shenoy S M, Blanchard J-M, Singer R H and Bertrand E 2003 Single mRNA molecules demonstrate probabilistic movement in living mammalian cells Curr. Biol. 13 1617 (Pubitemid 36154346)
2. Paulsson J 2004 Summing up the noise in gene networks Nature 427 4158 (Pubitemid 38168488)
3. Golding I, Paulsson J, Zawilski S M and Cox E C 2005 Real-time kinetics of gene activity in individual bacteria Cell 123 102536 (Pubitemid 41785418)
4. Yu J, Xiao J, Run X, Lao K and Xie X S 2006 Probing gene expression in live cells, one protein molecule at a time Science 311 16003
5. Arkin A, Ross J and McAdams H H 1998 Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells Genetics 149 163348 PMID: 9691025 (Pubitemid 28375939)
6. Murphy K F, Balazsi G and Collins J J 2007 Combinatorial promoter design for engineering noisy gene expression Proc. Natl Acad. Sci. USA 31 1272631 (Pubitemid 47255222)
7. Herbert K M, La Porta A, Wong B J, Mooney R A, Neuman K C, Landick R and Block S M 2006 Sequence-resolved detection of pausing by single RNA polymerase molecules Cell 125 108394 (Pubitemid 43866198)
8. Browning D F and Busby S J W 2004 The regulation of bacterial transcription initiation Nature Rev. Microbiol. 2 5765 (Pubitemid 39490048)
9. McClure W R 1985 Mechanism and control of transcription initiation in prokaryotes Annu. Rev. Biochem. 54 171204 (Pubitemid 15073645)
10. Saecker R M, Record M T and deHaseth P L 2011 Mechanism of bacterial transcription initiation: promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis J. Mol. Biol. 412 75471
11. Kennel D and Riezman H 1977 Transcription and translation initiation frequencies of the Escherichia coli lac operon J. Mol. Biol. 114 121 (Pubitemid 8149493)
12. Buc H and McClure W R 1985 Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps Biochemistry 24 271223 (Pubitemid 15016004)
13. Lutz R and Bujard H 1997 Independent and tight regulation of transcriptional units in Escherichia coli via the lacr/o, the tetr/o and arac/i1-i2 regulatory elements Nucl. Acids Res. 25 120310 (Pubitemid 27303212)
14. Lutz R, Lozinski T, Ellinger T and Bujard H 2001 Dissecting the functional program of Escherichia coli promoters: the combined mode of action of lac repressor and arac activator Nucl. Acids Res. 29 387381 (Pubitemid 32910527)
15. China A, Tare P and Nagaraja V 2010 Comparison of promoter-specific events during transcription initiation in mycobacteria Microbiology 156 194252
16. Taniguchi Y, Choi P J, Li G-W, Chen H, Babu M, Hearn J, Emili A and Xie X S 2010 Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329 5338
17. So L, Ghosh A, Zong C, Sepulveda L A, Segev R and Golding I 2011 General properties of transcriptional time series in Escherichia coli Nature Genet. 43 55460
18. Peccoud J and Ycart B 1995 Markovian modelling of gene product synthesis Theor. Popul. Biol. 48 22234
19. Yarchuk O, Jacques N, Guillerez J and Dreyfus M 1992 Interdependence of translation, transcription and mRNA J. Mol. Biol. 5 58196
20. Huh D and Paulsson J 2011 Non-genetic heterogeneity from stochastic partitioning at cell division Nature Genet. 43 95100
21. Huh D and Paulsson J 2011 Random partitioning of molecules at cell division Proc. Natl Acad. Sci. USA 108 150049
22. Lloyd-Price J, Lehtivaara M, Kandhavelu M, Chowdhury S, Muthukrishnan A-B, Yli-Harja O and Ribeiro A S 2011 Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli Mol. Biosyst. 8 56571
23. Llopis P M, Jackson A F, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T and Jacobs-Wagner C 2010 Spatial organization of the flow of genetic information in bacteria Nature 466 778
24. Golding I and Cox E C 2004 Rna dynamics in live Escherichia coli cells Proc. Natl Acad. Sci. USA 101 113105 (Pubitemid 39038343)
25. Chen T-B, Horng-Shing Lu H, Lee Y-S and Lan H-J 2008 Segmentation of cDNA microarray images by kernel density estimation J. Biomed. Inf. 41 10217
26. Otsu N 1979 A threshold selection method from gray-level histograms IEEE Trans. Syst. Man Cybern. 9 626 (Pubitemid 9413341)
27. Livak K and Schmittgen T 2001 Analysis of relative gene expression data using real-time quantitative PCR and the method Methods 25 4028 (Pubitemid 34164012)
28. Landick R 2006 The regulatory roles and mechanism of transcriptional pausing Biochem. Soc. Trans. 34 10626 (Pubitemid 46768989)
29. deHaseth P L, Zupancic M L and Record M T 1998 Rna polymerasepromoter interactions: the comings and goings of RNA polymerase J. Bacteriol. 180 301925 PMID: 9620948 (Pubitemid 28285012)
30. Hsu L M 2009 Monitoring abortive initiation Methods 47 2536
31. Ratcliff W C and Denison R F 2011 Bacterial persistence and bet hedging in Sinorhizobium meliloti Commun. Integr. Biol. 4 98100
32. Beaumont H J E, Gallie J, Kost C, Ferguson G C and Rainey P B 2009 Experimental evolution of bet hedging Nature 462 903
33. Lindner A B, Madden R, Demarez A, Stewart E J and Taddei F 2008 Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation Proc. Natl Acad. Sci. USA 105 307681 (Pubitemid 351723670)
34. Suter D M, Molina N, Gatfield D, Schneider K, Schibler U and Naef F 2011 Mammalian genes are transcribed with widely different bursting kinetics Science 332 4724
35. Harper C V et al 2011 Dynamic analysis of stochastic transcription cycles PLoS Biol. 9 e1000607
36. Ribeiro A S 2007 Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions Phys. Rev. E 75 061903
37. Ribeiro A S 2010 Stochastic and delayed stochastic models of gene expression and regulation Math. Biosci. 223 111