title: Genomic mining of prokaryotic repressors for orthogonal logic gates.
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 >10(54) 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.
authors: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors: Brynne C
authors: BC
authors: Stanton
authors: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors: Alec A K
authors: AA
authors: Nielsen
authors: Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA.
authors: Alvin
authors: A
authors: Tamsir
authors: Synthetic Biology R&D Unit, Life Technologies, Carlsbad, California, USA.
authors: Kevin
authors: K
authors: Clancy
authors: Synthetic Biology R&D Unit, Life Technologies, Carlsbad, California, USA.
authors: Todd
authors: T
authors: Peterson
authors: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors: Christopher A
authors: CA
authors: Voigt
mesh_terms: D001483:Base Sequence; D053263:Gene Regulatory Networks / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D009875:Operator Regions, Genetic; D011387:Prokaryotic Cells; D011401:Promoter Regions, Genetic / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics*; D054852:Small Molecule Libraries
chemical_list: D012097:Repressor Proteins; D054852:Small Molecule Libraries