Team:KULeuven/Model/Kinetic Constants

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This page contains various references to literature with several parameters that helped us get started on the model. More references, along with parameters can be found under the corresponding components sections.

Contents

ETHZ list of parameters

Bibliography

[1]“ETHZ/Parameters - IGEM07”; https://2007.igem.org/ETHZ/Parameters.
 

mRNA decay

Bibliography

[1]J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702.
 

T7 RNAP

Bibliography

[1]“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP.
 
[2]R. Ikeda, A. Lin, and J. Clarke, “Initiation of transcription by T7 RNA polymerase as its natural promoters,” J. Biol. Chem., vol. 267, Feb. 1992, pp. 2640-2649.
 
[3]R. Bandwar et al., “Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence,” Biochemistry, vol. 41, Mar. 2002, pp. 3586-3595.
 
[4]G.M. Skinner et al., “Promoter Binding, Initiation, and Elongation By Bacteriophage T7 RNA Polymerase: A SINGLE-MOLECULE VIEW OF THE TRANSCRIPTION CYCLE,” J. Biol. Chem., vol. 279, Jan. 2004, pp. 3239-3244.
 
[5]V.S. Anand and S.S. Patel, “Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase,” J. Biol. Chem., vol. 281, Nov. 2006, pp. 35677-35685.
 

LacI - LuxI

Bibliography

[1]M.B. Elowitz and S. Leibler, “A synthetic oscillatory network of transcriptional regulators,” Nature, vol. 403, Jan. 2000, pp. 335-338.
 
[2]“Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing,” Jul. 2004; http://www.pnas.org/content/101/30/10955.full.
 

LuxI, LuxR, mRNALuxI, mRNALuxR decay

Bibliography

[1]“Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein,” Sep. 1996; http://www.pnas.org/content/93/18/9505.
 
[2]L. Chen et al., “Noise-induced cooperative behavior in a multicell system,” Bioinformatics, vol. 21, Jun. 2005, pp. 2722-2729.
 

HSL stuff

Bibliography

[1]“Acyl homoserine-lactone quorum-sensing signal generation,” Apr. 1999; http://www.pnas.org/content/96/8/4360.full.
 
[2]P. Nilsson et al., “Kinetics of the AHL Regulatory System in a Model Biofilm System: How Many Bacteria Constitute a "Quorum"?,” Journal of Molecular Biology, vol. 309, Jun. 2001, pp. 631-640.
 
[3]Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” Appl. Environ. Microbiol., vol. 71, Mar. 2005, pp. 1291-1299.
 
[4]L. Wang et al., “Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-lactonase),” J. Biol. Chem., vol. 279, Apr. 2004, pp. 13645-13651.
 

Diffusion

Bibliography

[1]P.S. Stewart, “Diffusion in Biofilms,” J. Bacteriol., vol. 185, Mar. 2003, pp. 1485-1491.
 

OmpR, OmpF

Bibliography

[1]K.J. Huang, J.L. Schieberl, and M.M. Igo, “A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene.,” Journal of Bacteriology, vol. 176, Mar. 1994, pp. 1309–1315.
 
[2]K.V. Srividhya and S. Krishnaswamy, “A simulation model of Escherichia coli osmoregulatory switch using E-CELL system,” BMC Microbiology, vol. 4, 2004, p. 44.
 
[3]S.A. Forst, J. Delgado, and M. Inouye, “DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity.,” Journal of Bacteriology, vol. 171, Jun. 1989, pp. 2949–2955.
 
[4]N. Ramani, M. Hedeshian, and M. Freundlich, “micF antisense RNA has a major role in osmoregulation of OmpF in Escherichia coli.,” Journal of Bacteriology, vol. 176, Aug. 1994, pp. 5005–5010.
 
[5]T. Yoshida et al., “Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR,” J. Biol. Chem., vol. 281, Jun. 2006, pp. 17114-17123.
 
[6]S. Tokishita et al., “Transmembrane signal transduction and osmoregulation in Escherichia coli. Functional importance of the periplasmic domain of the membrane- located protein kinase, EnvZ,” J. Biol. Chem., vol. 266, Apr. 1991, pp. 6780-6785.
 

Psid met P2ogr promotor

Bibliography

[1]B. Julien and R. Calendar, “Bacteriophage PSP3 and phiR73 activator proteins: analysis of promoter specificities.,” Journal of Bacteriology, vol. 178, Oct. 1996, pp. 5668–5675.
 
[2]“Cambridge/Amplifier project - IGEM07”; https://2007.igem.org/Cambridge/Amplifier_project.
 

Constitutive promoters

  • Estimated transcription rate for J23105:[1]
  • Scale other transcription rate with table in parts registry.
  • Estimate the rate of transcription from a constitutive promotor family member.
Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor

E. coli transcription rates

Bibliography

[1]M. Bon, S.J. McGowan, and P.R. Cook, “Many expressed genes in bacteria and yeast are transcribed only once per cell cycle,” FASEB J., vol. 20, Aug. 2006, pp. 1721-1723.
 

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