Difference between revisions of "Degradation of C"
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|<math>d_{C}</math> | |<math>d_{C}</math> | ||
− | |<math>0-0.001</math> <ref name=" | + | |<math>0-0.001</math> <ref name="Takano2006"> [http://www.mrc-lmb.cam.ac.uk/genomes/awuster/wecb/Takano_2006.pdf E. Takano. ''γ-butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation.'' Current Opinion in Microbiology, 9(3):287–294, 2006.]</ref> <ref name="Chen2005"> [http://ac.els-cdn.com/S0168165605000295/1-s2.0-S0168165605000295-main.pdf?_tid=1214eff2-74f5-11e5-a95e-00000aacb35f&acdnat=1445103342_a62ad340ee40c16e2887cfe9a7818772 Chen CC., Riadi L., Suh S.J., Ohman D.E., Ju L.K. ''Degradation and synthesis kinetics of quorum-sensing autoinducer in Pseudomonas aeruginosa cultivation.'' J Biotechnol. 2005;117(1):1-10.]</ref> |
− | + | |<math> min^{-1} </math> <ref name="Weber2011"> [http://www.biomedcentral.com/content/pdf/1752-0509-5-11.pdf Weber M., Buceta J. ''Noise regulation by quorum sensing in low mRNA copy number systems.'' BMC Systems Biology 2011, 5:11]</ref> <ref name="Kaufmann2005"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544315/pdf/pnas-0408639102.pdf Kaufmann GF, Sartorio R, Lee SH, Rogers CJ, Meijler MM, Moss JA, Clapham B, Brogan AP, Dickerson TJ, Janda KD. ''Revisiting quorum sensing: Discovery of additional chemical and biological functions for 3-oxo-N-acylhomoserine lactones.'' Proc Natl Acad Sci U S A. 2005;102(2):309-14.]</ref> | |
|<math>6.7 \cdot 10^{-5} s^{-1}</math><ref name="Mehra2008"></ref><ref name="Chatterjee2011"></ref> | |<math>6.7 \cdot 10^{-5} s^{-1}</math><ref name="Mehra2008"></ref><ref name="Chatterjee2011"></ref> | ||
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and <math>6.7 \cdot 10^{-6}-6.7 \cdot 10^{-3} s^{-1}</math><ref name="Chatterjee2011"></ref>) | and <math>6.7 \cdot 10^{-6}-6.7 \cdot 10^{-3} s^{-1}</math><ref name="Chatterjee2011"></ref>) | ||
− | | In a study on global analysis of mRNA decay in gram positive bacteria by RNA-Seq, Kristoffersen et al. reported a range of values for the half-life (<math>t_{1/2}</math>) of mRNA in ''B. cereus'' between <math>1.9-5.6 min </math>, with a median of <math>2.4 min </math>. From these values we calculated the mRNA degradation rate of ''scbR'' as per <math>d_{mR}= \frac{ln(2)}{t_{1/2}}</math>, which resulted in a degradation rate constant value range <math>0.124-0.365 min^{-1} </math> and a median <math>0.29 min^{-1} </math>. | + | | Chen et al. empirically calculated the degradation rate of the autoinducer PAI2 in ''Pseudomonas aeruginosa'' cultures and reported a best-fit degradation constant of <math>0.195 h^{-1} = 0.00325 min^{-1}</math>. |
− | + | [[Image:DC-text.png|center|thumb|400px|Chen et al. 2005<ref name="Chen2005"></ref>]] | |
+ | |||
+ | In a study on global analysis of mRNA decay in gram positive bacteria by RNA-Seq, Kristoffersen et al. reported a range of values for the half-life (<math>t_{1/2}</math>) of mRNA in ''B. cereus'' between <math>1.9-5.6 min </math>, with a median of <math>2.4 min </math>. From these values we calculated the mRNA degradation rate of ''scbR'' as per <math>d_{mR}= \frac{ln(2)}{t_{1/2}}</math>, which resulted in a degradation rate constant value range <math>0.124-0.365 min^{-1} </math> and a median <math>0.29 min^{-1} </math>. | ||
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Revision as of 18:51, 17 October 2015
The SCB protein (C) degrades.
Contents
Chemical equation
Rate equation
Parameters
The parameter of this reaction is the degradation rate of C ().
Name | Value | Units | Value in previous GBL models [1] [2] | Remarks-Reference |
---|---|---|---|---|
[3] [4] | [5] [6] | [1][2]
(Range tested: ) (Bistability range: [1] and [2]) |
Chen et al. empirically calculated the degradation rate of the autoinducer PAI2 in Pseudomonas aeruginosa cultures and reported a best-fit degradation constant of Failed to parse (Cannot store math image on filesystem.): 0.195 h^{-1} = 0.00325 min^{-1}
.
In a study on global analysis of mRNA decay in gram positive bacteria by RNA-Seq, Kristoffersen et al. reported a range of values for the half-life () of mRNA in B. cereus between , with a median of . From these values we calculated the mRNA degradation rate of scbR as per , which resulted in a degradation rate constant value range and a median . |
Name | Value | Units | Origin | Remarks |
---|---|---|---|---|
[7] | Degradation rate of acyl-homoserine lactone (AHL) | The assumption that the degradation of SCB1 is slower than
AHL is made, as described in Takano(2006)[3] |
Parameters with uncertainty
The most plausible parameter value for the is decided to be and the confidence interval . This means that the mode of the PDF is 0.0002 and the range where 95% of the values are found is between and .
The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:
The location and scale parameters of the distribution are:
Parameter | μ | σ |
---|---|---|
References
- ↑ 1.0 1.1 1.2 S. Mehra, S. Charaniya, E. Takano, and W.-S. Hu. A bistable gene switch for antibiotic biosynthesis: The butyrolactone regulon in streptomyces coelicolor. PLoS ONE, 3(7), 2008.
- ↑ 2.0 2.1 2.2 A. Chatterjee, L. Drews, S. Mehra, E. Takano, Y.N. Kaznessis, and W.-S. Hu. Convergent transcription in the butyrolactone regulon in streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis. PLoS ONE, 6(7), 2011.
- ↑ 3.0 3.1 E. Takano. γ-butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation. Current Opinion in Microbiology, 9(3):287–294, 2006. Cite error: Invalid
<ref>
tag; name "Takano2006" defined multiple times with different content - ↑ 4.0 4.1 Chen CC., Riadi L., Suh S.J., Ohman D.E., Ju L.K. Degradation and synthesis kinetics of quorum-sensing autoinducer in Pseudomonas aeruginosa cultivation. J Biotechnol. 2005;117(1):1-10.
- ↑ Weber M., Buceta J. Noise regulation by quorum sensing in low mRNA copy number systems. BMC Systems Biology 2011, 5:11
- ↑ Kaufmann GF, Sartorio R, Lee SH, Rogers CJ, Meijler MM, Moss JA, Clapham B, Brogan AP, Dickerson TJ, Janda KD. Revisiting quorum sensing: Discovery of additional chemical and biological functions for 3-oxo-N-acylhomoserine lactones. Proc Natl Acad Sci U S A. 2005;102(2):309-14.
- ↑ S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold & R. Weiss. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134, 2005