Degradation of a

The mRNA of scbA (a) degrades.

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	Remarks-Reference
$d_{mA}$	$0.03−0.365$	$min^{-1}$	$0.0018 s^{-1} (0.108 min^{-1})$ $8.1 \cdot 10^{-4} s^{-1} (0.0486 min^{-1})$ Range tested: $6.6 \cdot 10^{-4}-1.2 \cdot 10^{-2} s^{-1}$ ($0.0396-0.72 min^{-1}$) Bistability range: $0.0016-0.019 s^{-1}$ ($0.096-1.14 min^{-1}$) and $4.1 \cdot 10^{-4}-1.6 \cdot 10^{-2} s^{-1}$ ($0.0246-0.96 min^{-1}$)	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 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 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. By assigning the appropriate weights to the parameter values and using the method described here, the appropriate probability distributions were designed.

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 $d_{mA}$ to $0.14 min^{-1}$, we wish to explore the full range of reported values and maybe even sample a small percentage of values outside the reported range. Thus, the Spread was set to $2.06$, which means that the range where 68.27% of the values are found is between $0.068$ and $0.29 min^{-1}$.

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

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
$d_{mA}$	$0.14$	$2.06$	$-1.5916$	$0.60824$