Engineering an allosteric transcription factor to respond to new ligands. Escherichia coli

Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. A major class of regulatory proteins is microbial allosteric transcription factors (aTFs), but aTF–inducer pairs are currently limited by those that naturally occur. Altering inducer specificity in these proteins is difficult because mutations that affect inducer binding may also disrupt allostery. Here, we engineer an aTF, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol or sucralose. We employ computational protein design, single-residue saturation mutagenesis, or random mutagenesis, along with multiplex assembly, and identify initial hits via a two-stage enrichment screen. Following activity maturation, we identify LacI variants with specificity to and induction by these new inducers comparable to that of wild-type LacI and its inducer, IPTG. The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits. Overall design: Identification of E. coli LacI protein variants depleted after negative selection by next-generation sequencing.