Difference between revisions of "Translation of R"

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== Parameters ==
 
== Parameters ==
  
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The parameter of this reaction is the translation rate of ScbR (<math>P_{R}</math>).
+
The parameter of this reaction is the translation rate of ScbR (<math>P_{R}</math>). The parameter values were derived from calculations of the protein translation rate based on genomic properties of ''Streptomyces coelicolor'' A3(2) and ''E.coli''.
  
−
{|class="wikitable"
+
{|class="wikitable"  
 
! Name
 
! Name
 
! Value
 
! Value
 
! Units
 
! Units
−
! Origin
+
! 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>
−
! Remarks
+
! Remarks-Reference
 
|-
 
|-
 
|<math>P_{R}</math>
 
|<math>P_{R}</math>
−
|<math>0.88</math> <ref name="Cox2004"> Cox RA. ''Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach.'' Microbiology. 2004 May;150(Pt 5):1413-26. </ref>  
+
|<math>0.165−5.86</math> <ref name="Cox2004"> [http://www.microbiologyresearch.org/docserver/fulltext/micro/150/5/1413.pdf?expires=1444755552&id=id&accname=guest&checksum=009138F0691A4CE7FF9CB3F361C4DC87 Cox RA. ''Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach.'' Microbiology. 2004 May;150(Pt 5):1413-26.] </ref>
−
|<math> min^{-1} </math>
+
|<math> min^{-1} </math>  
−
| ''Streptomyces coelicolor'' A3(2)
+
|<math>0.36 s^{-1}</math>
−
| Translation values were calculated according to the rates proposed in the paper by R.A. Cox using the basepairs for each gene.For scbR the initiation rate is 5 <math> min^{-1} </math> and the elongation rate is (648/3-1 aa/gene)/(14 aa/<math>s^{-1}</math>)= , thus resulting in a final value of 0.88 <math> min^{-1} </math>.  
+
 
−
Since the elongation is slower than the initiation, we conclude that it is the limiting step.
+
<math>(21.6 min^{-1})</math><ref name="Mehra2008"></ref><ref name="Chatterjee2011"></ref>
 +
 
 +
Range tested:
 +
 
 +
<math>10^{-4}-10 s^{-1}</math>
 +
 
 +
(<math>0.0001-600 min^{-1}</math>)
 +
 
 +
Bistability range:
 +
 
 +
<math>0.25-0.39 s^{-1}</math><ref name="Mehra2008"></ref>
 +
 
 +
(<math>15-23.4 min^{-1}</math>)
 +
 
 +
and <math>0.09-0.38 s^{-1}</math><ref name="Chatterjee2011"></ref>
 +
 
 +
(<math>5.4-22.8 min^{-1}</math>)
 +
| In a recent publication by R.A. Cox, genomic properties and macromolecular compositions of ''Streptomyces coelicolor'' A3(2) and ''E.coli'' were reported, along with equations that connect these properties. For ''S. coelicolor'', the polypeptide elongation rate <math>ε_{aa}</math> is reported to be in the range between 0.59 and 3.17 amino acids s<sup>-1</sup>. As ScbR has 215 aa, the transcription rate constant can be calculated as per <math>P_{R}=\frac{215 aa/gene}{0.59 aa/s}=364.4 s/gene=6.07 min/gene</math> and <math>P_{R}=\frac{215 aa/gene}{3.17 aa/s}=67.82 s/gene=1.13 min/gene</math>, thus resulting in a final value of <math> 0.165 min^{-1} </math> and <math> 0.89 min^{-1} </math>.  
 +
<div><ul>
 +
<li style="display: inline-block;"> [[Image:TR-text.png|center|thumb|700px|Cox et al. 2004<ref name="Cox2004"></ref>]] </li>
 +
<li style="display: inline-block;"> [[Image:TR-text2.png|center|thumb|700px|Cox et al. 2004<ref name="Cox2004"></ref>]] </li>
 +
</ul></div>
 +
 
 +
Additionally, Cox reports translation rates for ''E. coli'' between 12 and 21 aa/s. By the same calculations, the corresponding transcription rate constants are in the range <math> 3.35-5.86 min^{-1} </math>.
 +
[[Image:PR-text.png|center|thumb|700px|Cox et al. 2004<ref name="Cox2004"></ref>]]
 
|}
 
|}
  
 
==Parameters with uncertainty==
 
==Parameters with uncertainty==
  
−
The most plausible parameter value for the <math>P_{R}</math> is decided to be <math> 0.5 min^{-1} </math> and the confidence interval <math>10</math>. This means that the mode of the PDF is 0.5 and the range where 95% of the values are found is between 0.05 and 5 <math>min^{-1}</math>.
+
When deciding how to describe the uncertainty for this parameter we must take into consideration the fact that the reported values are either calculated or derived with approximation from experiments and from other macromolecular properties. Additionally, some of the values correspond to protein translation rates of different bacteria species (''E. coli''). This means that there might be a notable difference between actual parameter values and the ones reported in literature. These facts influence the quantification of the parameter uncertainty and therefore the shape of the corresponding distribution.
 +
 
 +
Therefore, although the weight of the distribution is put on the values calculated for ''S. coelicolor'' by setting <math> 0.74 min^{-1} </math> as the mode of the log-normal distribution for the <math>P_{R}</math>, we wish to explore the full range of reported values. Thus, the Spread is set to <math>3.2</math> and the range where 68.27% of the values are found is between <math>0.23</math> and <math>2.38</math> <math>min^{-1}</math>.
  
 
The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:
 
The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:
  
−
[[Image:PR.png|500px]]
+
[[Image:PRu.png|500px]]
 +
 
 +
The values retrieved from literature and their weights are indicated by the blue dashed lines, and the uncertainty for each value is indicated using a default value of 10% error (orange lines).
  
−
The location and scale parameters of the distribution are:
+
The parameter information of the distribution is:
 
{|class="wikitable"
 
{|class="wikitable"
 
! Parameter
 
! Parameter
 +
! Mode
 +
! Spread
 
! μ
 
! μ
 
! σ
 
! σ
 
|-
 
|-
 
|<math>P_{R}</math>
 
|<math>P_{R}</math>
−
|<math>0.1220</math>
+
|<math>0.744</math>
−
|<math>0.9028</math>
+
|<math>3.2</math>
 +
|<math>0.42952</math>
 +
|<math>0.85176</math>
 
|}
 
|}
  
 
==References==
 
==References==
 
<references/>
 
<references/>

Latest revision as of 15:53, 4 January 2018

The scbR mRNA (r) is translated into ScbR protein (R).

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About this image

Chemical equation

r \rightarrow r + R

Rate equation

r= P_{R}\cdot [r]

Parameters

The parameter of this reaction is the translation rate of ScbR (P_{R}). The parameter values were derived from calculations of the protein translation rate based on genomic properties of Streptomyces coelicolor A3(2) and E.coli.

Name Value Units Value in previous GBL models [1] [2] Remarks-Reference
P_{R} 0.165−5.86 [3] min^{-1} 0.36 s^{-1}

(21.6 min^{-1})[1][2]

Range tested:

10^{-4}-10 s^{-1}

(0.0001-600 min^{-1})

Bistability range:

0.25-0.39 s^{-1}[1]

(15-23.4 min^{-1})

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

(5.4-22.8 min^{-1})

In a recent publication by R.A. Cox, genomic properties and macromolecular compositions of Streptomyces coelicolor A3(2) and E.coli were reported, along with equations that connect these properties. For S. coelicolor, the polypeptide elongation rate ε_{aa} is reported to be in the range between 0.59 and 3.17 amino acids s-1. As ScbR has 215 aa, the transcription rate constant can be calculated as per P_{R}=\frac{215 aa/gene}{0.59 aa/s}=364.4 s/gene=6.07 min/gene and P_{R}=\frac{215 aa/gene}{3.17 aa/s}=67.82 s/gene=1.13 min/gene, thus resulting in a final value of 0.165 min^{-1} and 0.89 min^{-1} .
  • Cox et al. 2004[3]
  • Cox et al. 2004[3]

Additionally, Cox reports translation rates for E. coli between 12 and 21 aa/s. By the same calculations, the corresponding transcription rate constants are in the range 3.35-5.86 min^{-1} .

Cox et al. 2004[3]

Parameters with uncertainty

When deciding how to describe the uncertainty for this parameter we must take into consideration the fact that the reported values are either calculated or derived with approximation from experiments and from other macromolecular properties. Additionally, some of the values correspond to protein translation rates of different bacteria species (E. coli). This means that there might be a notable difference between actual parameter values and the ones reported in literature. These facts influence the quantification of the parameter uncertainty and therefore the shape of the corresponding distribution.

Therefore, although the weight of the distribution is put on the values calculated for S. coelicolor by setting 0.74 min^{-1} as the mode of the log-normal distribution for the P_{R}, we wish to explore the full range of reported values. Thus, the Spread is set to 3.2 and the range where 68.27% of the values are found is between 0.23 and 2.38 min^{-1}.

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

PRu.png

The values retrieved from literature and their weights are indicated by the blue dashed lines, and the uncertainty for each value is indicated using a default value of 10% error (orange lines).

The parameter information of the distribution is:

Parameter Mode Spread μ σ
P_{R} 0.744 3.2 0.42952 0.85176

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 3.2 3.3 Cox RA. Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach. Microbiology. 2004 May;150(Pt 5):1413-26.
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