Genomic mining of prokaryotic repressors for orthogonal logic gates

BC Stanton, AAK Nielsen, A Tamsir, K Clancy… - Nature chemical …, 2014 - nature.com
BC Stanton, AAK Nielsen, A Tamsir, K Clancy, T Peterson, CA Voigt
Nature chemical biology, 2014nature.com
Genetic circuits perform computational operations based on interactions between freely
diffusing molecules within a cell. When transcription factors are combined to build a circuit,
unintended interactions can disrupt its function. Here, we apply'part mining'to build a library
of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset
were determined using an in vitro method, and this information was used to build synthetic
promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 …
Abstract
Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method, and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and exhibit minimal interactions with other promoters. Each repressor-promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOT/NOR gates, there are >1054 circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits.
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