Effects of Rate-Limiting Steps in Transcription Initiation on Genetic Filter Motifs

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Häkkinen, Antti ^a   Tran, Huy ^a   Yli Harja, Olli ^a,b   Ribeiro, Andre S ^a  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ALGORITHM; AMPLITUDE MODULATION; ARTICLE; FREQUENCY MODULATION; GENE INTERACTION; GENE PRODUCT; GENE REPRESSION; GENE STRUCTURE; GENETIC REGULATION; MATHEMATICAL ANALYSIS; PLASTICITY; PROBABILITY; PROMOTER REGION; SIGNAL NOISE RATIO; STOCHASTIC MODEL; TRANSCRIPTION INITIATION;

ANIMALS; GENE EXPRESSION REGULATION, BACTERIAL; HUMANS; MODELS, GENETIC; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 84881090097     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070439     Document Type: Article

References (17)

1. Wolf DM, Arkin AP, (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol 6: 125-134.
2. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
3. Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN, (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99: 9697-9702.
4. McClure WR, (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54: 171-204.
5. Lutz R, Lozinski T, Ellinger T, 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: 3873-3881.
6. Kandhavelu M, Mannerstrom H, Gupta A, Hakkinen A, Lloyd-Price J, et al. (2011) In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli: Evidence for a sequential mechanism with two rate-limiting steps. BMC Syst Biol 5: 149.
7. Muthukrishnan AB, Kandhavelu M, Lloyd-Price J, Kudasov F, Chowdhury S, et al. (2012) Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells. Nucleic Acids Res 40: 8472-8483.
8. Pedraza JM, Paulsson J, (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science 319: 339-343.
9. Ribeiro AS, Zhu R, Kauffman SA, (2006) A general modeling strategy for gene regulatory networks with stochastic dynamics. J Comp Biol 13: 1630-1639.
10. Roussel MR, Zhu R, (2006) Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression title. Phys Biol 3: 274-284.
11. Ribeiro AS, Lloyd-Price J, (2007) Sgn sim, a stochastic genetic networks simulator. Bioinf 23: 777-779.
12. deHaseth PL, Zupancic ML, Record MT Jr, (1998) Rna polymerase-promoter interactions: The comings and goings of rna polymerase. J Bacteriol 180: 3019-3025.
13. Xia K, Manning M, Hesham H, Lin Q, Bystroff C, et al. (2007) Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE. Proc Natl Acad Sci USA 104: 17329-17334.
14. Dyson S, Gurdon JB, (1998) The interpretation of position in a morphogen gradient as revealed by occupancy of activin receptors. Cell 93: 557-568.
15. Loinger A, Biham O, (2007) Stochastic simulations of the repressilator circuit. Phys Rev E 76: 051917.
16. Kandhavelu M, Häkkinen A, Yli-Harja O, Ribeiro AS, (2012) Single-molecule dynamics of transcription of the lar promoter. Phys Biol 9: 026004.
17. Ribeiro AS, Hakkinen A, Mannerstrom H, Lloyd-Price J, Yli-Harja O, (2010) Effects of the promoter open complex formation on gene expression dynamics. Phys Rev E 81: 011912.