As synthetic regulatory programs expand in sophistication, an ever increasing number of biological components with predictable phenotypes is required. Regulators are often ‘part mined’ from a diverse, but uncharacterized, array of genomic sequences, often leading to idiosyncratic behavior. Here, we generate an entire synthetic phylogeny from the canonical allosteric transcription factor TrpR. Iterative rounds of positive and negative compartmentalized partnered replication (CPR) led to the exponential amplification of variants that responded with high affinity and specificity to halogenated tryptophan analogs and novel operator sites. Fourteen repressor variants were evolved with unique regulatory profiles across five operators and three ligands. The logic of individual repressors can be modularly programmed by creating heterodimeric fusions, resulting in single proteins that display logic functions, such as ‘NAND’. Despite the evolutionarily limited regulatory role of TrpR, vast functional spaces exist around this highly conserved protein scaffold and can be harnessed to create synthetic regulatory programs.

随着合成调节程序在复杂性方面的扩展，需要数量越来越多且具有可预测表型的生物成分。调节子通常是“挖矿”于各种不同但未表征的基因组序列中，常常导致特质行为。在这里，我们从典型的变构转录因子TrpR生成了一个完整的系统发育史。阳性和阴性间隔部分配对复制（CPR）的迭代回合导致对卤代色氨酸类似物和新型操纵基因位点具有高亲和力和特异性的变异体的指数扩增。在五个操作员和三个配体之间进化出具有独特调节特性的14个阻遏物变体。单个阻遏物的逻辑可以通过创建异二聚体融合进行模块化编程，产生具有逻辑功能的单一蛋白质，例如“ NAND”。尽管TrpR的调控作用在进化上受到限制，但在高度保守的蛋白支架周围仍存在巨大的功能空间，可以利用这些功能空间来创建合成的调控程序。