Difference between revisions of "Degradation of a"

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== Parameters ==
 
== Parameters ==
  
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The parameter of this reaction is the degradation rate of a (<math>d_{mA}</math>).
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The parameter of this reaction is the degradation rate of a (<math>d_{mA}</math>). The parameter values were derived from calculations of the mRNA half life in gram positive bacteria with low GC content and in ''Actinomycetes''.
  
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{|class="wikitable"
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{|class="wikitable"  
 
! Name
 
! Name
 
! Value
 
! Value
 
! Units
 
! Units
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! Origin
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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
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! Remarks-Reference
 
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|-
 
|<math>d_{mA}</math>
 
|<math>d_{mA}</math>
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|<math>0.045-0.4 </math> <ref name="Kristoffersen2012"> Kristoffersen SM, Haase C, Weil MR, et al. ''Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium.'' Genome Biology. 2012;13(4):R30.</ref> <ref name="Ortiz2007"> Ortiz-Ortiz, L. and Bojalil, L.F. and Yakoleff, V. ''Biological, Biochemical, and Biomedical Aspects of Actinomycetes.'' Elsevier, 2013</ref>  
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|<math>0.03-0.4</math> <ref name="Kristoffersen2012"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446304/pdf/gb-2012-13-4-r30.pdf Kristoffersen SM, Haase C, Weil MR, et al. ''Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium.'' Genome Biology. 2012;13(4):R30.]</ref> <ref name="Ortiz1984"> [http://www.sciencedirect.com/science/book/9780125286206 Ortiz-Ortiz, L. and Bojalil, L.F. and Yakoleff, V. ''Biological, Biochemical, and Biomedical Aspects of Actinomycetes.'' Elsevier, 1984]</ref>
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| <math>min^{-1}</math>
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|<math> min^{-1} </math>  
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| Half life of mRNA in Gram positive bacteria (low GC content)
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|<math>0.0018 s^{-1}</math><ref name="Mehra2008"></ref>
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Half life of mRNA in Actinomycetes
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<math>8.1 \cdot 10^{-4} s^{-1}</math><ref name="Chatterjee2011"></ref>
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|  
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(Range tested: <math>6.6 \cdot 10^{-4}-1.2 \cdot 10^{-2} s^{-1}</math>)
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(Bistability range: <math>0.0016-0.019 s^{-1}</math><ref name="Mehra2008"></ref>
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and <math>4.1 \cdot 10^{-4}-1.6 \cdot 10^{-2} 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 ''scbA'' as per <math>d_{mA}= /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|500px|Kristoffersen et al. 2012<ref name="Kristoffersen2012"></ref>]]
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Additionally, in a book on biological and biochemical aspects of ''Actinomycetes'', Ortiz-Ortiz et al. reported a range of mRNA degradation rates for ''Streptomyces antibioticus'' spores between <math>4-22.5 min </math>. By the same calculations, the corresponding mRNA degradation rate constants are in the range <math> 0.031-0.17 min^{-1} </math>.
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[[Image:DmR-text2.png|center|thumb|500px|Ortiz-Ortiz et al. 1984<ref name="Ortiz1984"></ref>]]
 
|}
 
|}
  

Revision as of 07:03, 16 October 2015

The mRNA of scbA (a) degrades.

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About this image

Chemical equation

a\rightarrow \varnothing

Rate equation

r= d_{mA}\cdot[a]

Parameters

The parameter of this reaction is the degradation rate of a (d_{mA}). The parameter values were derived from calculations of the mRNA half life in gram positive bacteria with low GC content and in Actinomycetes.

Name Value Units Value in previous GBL models [1] [2] Remarks-Reference
d_{mA} 0.03-0.4 [3] [4] min^{-1} 0.0018 s^{-1}[1]

8.1 \cdot 10^{-4} s^{-1}[2]

(Range tested: 6.6 \cdot 10^{-4}-1.2 \cdot 10^{-2} s^{-1})

(Bistability range: 0.0016-0.019 s^{-1}[1]

and 4.1 \cdot 10^{-4}-1.6 \cdot 10^{-2} 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 scbA as per d_{mA}= /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[3]

Additionally, in a book on biological and biochemical aspects of Actinomycetes, Ortiz-Ortiz et al. reported a range of mRNA degradation rates for Streptomyces antibioticus spores between 4-22.5 min . By the same calculations, the corresponding mRNA degradation rate constants are in the range 0.031-0.17 min^{-1} .

Ortiz-Ortiz et al. 1984[4]

Parameters with uncertainty

The most plausible parameter value for the d_{mR} is decided to be 0.1785 min^{-1} and the confidence interval 1.55 . This means that the mode of the PDF is 0.1785 and the range where 95% of the values are found is between 0.1156 and 0.277 min^{-1}.

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

500px

The location and scale parameters of the distribution are:

Parameter μ σ
d_{mA} -1.6753 0.2187

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 Kristoffersen SM, Haase C, Weil MR, et al. Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium. Genome Biology. 2012;13(4):R30.
  4. ↑ 4.0 4.1 Ortiz-Ortiz, L. and Bojalil, L.F. and Yakoleff, V. Biological, Biochemical, and Biomedical Aspects of Actinomycetes. Elsevier, 1984
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