Degradation of r

The mRNA of scbR (r) degrades.

Chemical equation

$r\rightarrow \varnothing$

Rate equation

$r= d_{mR}\cdot[r]$

Parameters

The parameter of this reaction is the degradation rate of r ($d_{mR}$). 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	Remarks-Reference
$d_{mR}$	$0.11-4$	$min^{-1}$	$0.0018 s^{-1}$ $0.007 s^{-1}$ (Range tested: $6.6 \cdot 10^{-4}-1.2 \cdot 10^{-2} s^{-1}$) (Bistability range: $0.0016-0.019 s^{-1}$ and $3.5 \cdot 10^{-4}-1.4 \cdot 10^{-2} s^{-1}$)	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 ($t_1/2$) 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 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

Name	Value	Units	Origin	Remarks
$d_{mR}$	$0.045-0.4$	$min^{-1}$	Half life of mRNA in Gram positive bacteria (low GC content) Half life of mRNA in Actinomycetes

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:

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The location and scale parameters of the distribution are:

Parameter	μ	σ
$d_{mR}$	$-1.6753$	$0.2187$