Difference between revisions of "Degradation of R"

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The parameter of this reaction is the degradation rate of R (<math>d_{R}</math>).
 
The parameter of this reaction is the degradation rate of R (<math>d_{R}</math>).
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{|class="wikitable"
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! Name
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! Value
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! Units
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! Value in previous GBL models <ref name="Mehra2008"> [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0002724&representation=PDF 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.] </ref> <ref name="Chatterjee2011"> [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0021974&representation=PDF 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.] </ref>
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! Remarks-Reference
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|<math>d_{R}</math>
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|<math>0.03-0.4</math> <ref name="Trötschel2013"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815937/pdf/mbt0006-0708.pdf Trötschel C, Albaum SP, Poetsch A. ''Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria.'' Microbial biotechnology. 2013;6(6):708-719.]</ref> <ref name="Jayapal2010"> [http://pubs.acs.org/doi/pdf/10.1021/pr9007738 Jayapal KP, Sui S, Philp RJ, Kok YJ, Yap MG, Griffin TJ, Hu WS. ''Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems.'' J Proteome Res. 2010 May 7;9(5):2087-97.]</ref>
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|<math> min^{-1} </math>
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|<math>0.004 s^{-1}</math><ref name="Mehra2008"></ref>
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<math>0.36 s^{-1}</math><ref name="Chatterjee2011"></ref>
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(Range tested: <math>10^{-7}-10^{-1} s^{-1}</math>)
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(Bistability range: <math>0.0022-0.0067 s^{-1}</math><ref name="Mehra2008"></ref>
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and <math>0.09-0.38 s^{-1}</math><ref name="Chatterjee2011"></ref>)
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| 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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[[Image:DmR-text.png|center|thumb|600px|Kristoffersen et al. 2012<ref name="Kristoffersen2012"></ref>]]
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{|class="wikitable"

Revision as of 16:40, 16 October 2015

The ScbR monomer (R) degrades.

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About this image

Chemical equation

R\rightarrow \varnothing

Rate equation

r= d_{R}\cdot[R]

Parameters

The parameter of this reaction is the degradation rate of R (d_{R}).

Name Value Units Value in previous GBL models [1] [2] Remarks-Reference
d_{R} 0.03-0.4 [3] [4] min^{-1} 0.004 s^{-1}[1]

0.36 s^{-1}[2]

(Range tested: 10^{-7}-10^{-1} s^{-1})

(Bistability range: 0.0022-0.0067 s^{-1}[1]

and 0.09-0.38 s^{-1}[2])

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 (t_{1/2}) of mRNA in B. cereus between 1.9-5.6 min , with a median of 2.4 min . From these values we calculated the mRNA degradation rate of scbR as per d_{mR}= \frac{ln(2)}{t_{1/2}}, which resulted in a degradation rate constant value range 0.124-0.365 min^{-1} and a median 0.29 min^{-1} .
Kristoffersen et al. 2012[5]
Name Value Units Origin Remarks
d_{R} 0.000833-0.001667 [3] min^{-1} Degradation rates of proteins in S. coelicolor

based on radioactive decay

Parameters with uncertainty

The most plausible parameter value for the d_{R} is decided to be 0.00118 min^{-1} and the confidence interval 1.41 . This means that the mode of the PDF is 0.00118 and the range where 95% of the values are found is between 0.8369\cdot 10^{-3} and 1.67 \cdot 10^{-3}min^{-1}.

The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:

DR.png

The location and scale parameters of the distribution are:

Parameter μ σ
d_{R} -6.7120 0.174

References

  1. ↑ 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. ↑ 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. ↑ 3.0 3.1 Trötschel C, Albaum SP, Poetsch A. Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria. Microbial biotechnology. 2013;6(6):708-719. Cite error: Invalid <ref> tag; name "Tr.C3.B6tschel2013" defined multiple times with different content
  4. ↑ Jayapal KP, Sui S, Philp RJ, Kok YJ, Yap MG, Griffin TJ, Hu WS. Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems. J Proteome Res. 2010 May 7;9(5):2087-97.
  5. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named Kristoffersen2012
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