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
$d_{mR}$	$0.03-0.4$	$min^{-1}$	$0.0017 s^{-1}$ $0.007 s^{-1}$ (Range tested: $6.6 \cdot 10^{-4}-1.2 \cdot 10^{-2} s^{-1}$) (Bistability range: $0.0015-0.0025 s^{-1}$ 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

Parameters with uncertainty

When deciding how to describe the uncertainty for this parameter we must take into consideration that the reported values are either calculated or derived with approximation from experiments. Additionally they correspond to mRNA degradation rates of different bacteria species (B. cereus) and to unstable mRNA in S. antibioticus spores. This means that there might be a notable difference between the 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 the Streptomyces species by setting the mode of the log-normal distribution of the $d_{mR}$ to $0.15 min^{-1}$, we wish to explore the full range of reported values and maybe even sample a small percentage of values outside the reported range. Therefore, the confidence interval factor was set to $3$, which means that the range where 95% of the values are found is between $0.05$ and $0.45 min^{-1}$.

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
$d_{mR}$	$-1.6927$	$0.5229$