Team:ULB-Brussels/Modelling/2A-Peptid

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Revision as of 13:25, 20 September 2014

$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \newcommand{\MyColi}{{\small Mighty\hspace{0.12cm}Coli}} \newcommand{\Stabi}{\small Stabi}$ $\newcommand{\EColi}{\small E.coli} \newcommand{\SCere}{\small S.cerevisae}\\[0cm] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \newcommand{\PI}{\small PI}$ $\newcommand{\Igo}{\Large\mathcal{I}} \newcommand{\Tgo}{\Large\mathcal{T}} \newcommand{\Ogo}{\Large\mathcal{O}} ~$

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Previous Years 2012 : InteGreator 2011 : Pindel 2010 : HydroColi 2009 : GluColi

-Du nouveau pour comparer avec et sans p2A? Yes, now we get it!

- Université Libre de Bruxelles - 2A Peptide $\newcommand{\Tox}{\small Tox} \newcommand{\AnTox}{\small Anti\hspace{0.08cm} Tox} \newcommand{\EColi}{\small E.Coli}$ Now we're ready to compare our $\MyColi$ with the usual $\Stabi$ system. The objective of $\Stabi$ is to stabilize the presence of the plasmids that contain the $\PI$ gene sequence. $\EColi$ can insert other plasmids, containing the $\Tox$ and the $\AnTox$ genes. These two proteins are produced at same rate (contitutive promoter: T7) and the $\PI$ is independently produced in this classical system. The objective of $\MyColi$ is a little bit different: The T7 promoter iniciates the transcription of the $\PI$ $\small\&$ the $\AnTox$ genes, but another promoter, pBAD, controls the transcription of the $\Tox$ gene, situated in another plasmid than the $\PI$ $\small\&$ the $\AnTox$ genes. The problem with the classical system is that if there are a lot of mutations or a lot of heterogeneity in the $\EColi$ population, the $\PI$ is not produced at high rate. In a bioreactor built to product a special kind of $\PI$, this system's not optimal because there're $\PI$ losses, especially if the $\PI$ gene sequence is long or if the $\PI$ is cumbersome for $\EColi$. With our $\MyColi$ system, the sub-producing bacteria are eliminated from the bioreactor because these $\EColi$ don't produce the $\PI$ in sufficient quantity (the $\PI$ is produced at same rate than the $\AnTox$, thanks to the $2A$ $peptid$). Because the presence of the $p2A$ is necessary with $\MyColi$, the losses can be divided in two classes: (1) bacteria without cleavage of p2A $\hspace{0.1cm}\small\&\hspace{0.1cm}$ (2) bacteria killed by TA system, when there's more $\Tox$ than $\AnTox$ (this's when the fraction [$\Tox$]/[$\AnTox$] is bigger than one, this happens when a lot of $\AnTox$ are degraded and when $Tox$ is produced at high rate). To only take a sight in the $\MyColi$ mechanism, we'll assume that $\EColi$ is virtually immortal (no relation between the producing rate of proteins and the old age of some members of the population), that $\EColi$ have food when the bioreactor is working and that $\Tox$ and $\AnTox$ recombine rapidly in TA-complex (no dependence with the mean free path of proteins into the cytoplasm). Our 4 parameters are (a) the probability of mutations in comparison with the length of the genes, (b) the estimator of the heterogeneity in populations, (c) the cleavage rate of p2A, (d) the proportion of bacteria died by the TA-system in comparison with the fraction [$\Tox$]/[$\AnTox$]. A problem with $\MyColi$ is that the bioreactor cannot stop, because when it stops, tha antitoxin is not produced and bacteria die. A solution to this is the tranfer the bacteria from a growth medium with arabinose to a growth medium with glucose, because $\small ara$ activates pBAD and $\small glu$ stops $pBAD$ (as proven by experiments in our previous Results page).
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