Systems Biology - Methods - Transcriptomics

From Keaslingwiki

The incorporation of an exogenous biochemical pathway into a host places an unregulated strain on the cell by consuming central metabolites, energy and critical cofactors. Escherichia coli has evolved over the millennia to optimize its metabolism under many growth conditions in order to maximize survivability. Thus the cell has a large network of sensor and regulatory elements at its disposal and will respond rapidly to any change in the intra- or extra- cellular environment. The E. coli host will often sense an engineered pathway via some imbalance in the metabolite pool. This imbalance will trigger a variety of stress response systems which the cell has evolved in the context of its wild type environment. While these stress responses may be useful to the cell in a mammalian gut, they are unfavorable in an engineering context and reduce product yield or viability in a production fermentor. Until very recently, it has been difficult to really understand the impact of an exogenous pathway on the host within the context of its full metabolism. The advent of transcriptional profiling however has made it possible to measure how a metabolite imbalance propagates through the cellular regulatory network. A DNA microarray provides data on the relative expression level of every gene in E. coli at a given moment by measuring the number of mRNA copies of each open reading frame. Using this data we can determine how the cell perceives and responds to the strain of the engineered pathway. Thus transcriptomics provides a window into the regulation of cell physiology and allows us as engineers to understand the effects of synthetic alterations to endogenous metabolism. --Lance

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