Team:UNAM Genomics Mexico/Project/Overview


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Project Overview

Cells receive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate specific genetic responses. The expression of a gene is regulated by other proteins (Transcription Factors). This regulation is due to the interaction between TFs and their binding sites on DNA sequences, which inhibits or promotes the binding of RNA polymerase to the gene to start transcription.

Regulation can be quantified by the "response characteristics", meaning the level of gene expression as a function of the concentration of (activated) TFs. Although we consider protein concentration as a continuous variable, essential features of the response characteristics can often be represented more compactly by a binary "logic function", which specifies whether a gene is "ON" (expressed) or "OFF" (silent, or expressed at basal level) at different extremes of cellular TF concentrations.[1]

Bacillus Booleanus was born as a project in which we were going to create several boolean operations following one another, specifically, two ANDs and one OR. Obviously, as with any other project, it came a time when we had to ask ourselves, how on Earth were we going to accomplish that?. Of course, quorum sensing has always been a common choice in the iGEM community when it comes to boolean operations, but we decided to try another perspective, and ta-da! Bacillus booleanus was born! We took advantage of the super-powers reported to exist in Bacillus subtilis by Ben-Yehuda et al. [2] to establish this communication. Probably the unsuspecting reader is asking herself, what could this said super-powers be? Well, in 2011, Ben-Yehuda et al. showed that Bacillus subtilis was capable of creating nanotubes between and within strains to send relatively big proteins and communicate between them. Who says that we are living in an isolating era?

Well, since these super-powers were not enough to fight crime, we decided better to insert into the chromosomes of two different strains of our beloved bacterium the same transcription factor, but regulated by two different promoters, each needing two input signals to be activated (imitating the computational ANDs), and in another strain a promoter that was activated by this transcription factor (imitating the OR).

Then, Bacillus subtilis (imitating Houdini) would make its magic and the different strains would communicate, creating a connection between three different Boolean operations. This would make us really happy.

[1]Buchler et al. On schemes of combinatorial transcription logic print April 17, 2003, doi: 10.1073/pnas.0930314100 PNAS April 29, 2003 vol. 100 no. 9 5136-5141


[2] Dubey GP, Ben -Yehuda S.; Intercellular nanotubes mediate bacterial communication. Cell. 2011; 144(4):590-600.