Difference between revisions of "Degradation of R"

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== Parameters ==
 
== Parameters ==
  
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The parameter of this reaction is the degradation rate of R (<math>d_{R}</math>).
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The parameter of this reaction is the degradation rate of R (<math>d_{R}</math>). The parameter values were derived from proteomics studies on different proteins of S. coelicolor.
  
 
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and <math>0.09-0.38 s^{-1}</math><ref name="Chatterjee2011"></ref>)
 
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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|In a quantitative proteomics study on protein turnover rates in dynamic systems, Jayapal et al. reported the degradation rates of 115 proteins in ''S. coelicolor'' cultures undergoing transition from exponential growth to stationary phase. The values were in the range <math>0.05-0.22 h^{-1} (8.3 \cdot 10^{-4}-0.0037 min^{-1}) </math> with a median of <math>0.097 h^{-1} (0.00162 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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[[Image:DR-text.png|center|thumb|600px|Jayapal et al. 2012<ref name="Jayapal2010"></ref>]]
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! Name
 
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! Value
 
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! Units
 
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! Origin
 
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! Remarks
 
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|<math>d_{R}</math>
 
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|<math>0.000833-0.001667</math> <ref name="Trötschel2013"> 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>
 
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| <math>min^{-1}</math>
 
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| Degradation rates of proteins in ''S. coelicolor''
 
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based on radioactive decay
 
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Revision as of 17:20, 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}). The parameter values were derived from proteomics studies on different proteins of S. coelicolor.

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 quantitative proteomics study on protein turnover rates in dynamic systems, Jayapal et al. reported the degradation rates of 115 proteins in S. coelicolor cultures undergoing transition from exponential growth to stationary phase. The values were in the range 0.05-0.22 h^{-1} (8.3 \cdot 10^{-4}-0.0037 min^{-1}) with a median of 0.097 h^{-1} (0.00162 min^{-1}).
Jayapal et al. 2012[4]

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. ↑ 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.
  4. ↑ 4.0 4.1 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.
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