Predicting Transcriptional Output of Synthetic Multi-input Promoters

Recent advances in synthetic biology have led to a wealth of well-characterized genetic parts. As parts libraries grow, so too does the potential to create novel multi-input promoters that integrate disparate signals to determine transcriptional output. Our ability to construct such promoters will outpace our ability to characterize promoter performance, due to the vast number of input combinations. In this study, we examine the input-output relations of recently developed synthetic multi-input promoters and describe two methods for predicting their behavior. The first method uses 1-dimensional induction data obtained from experiments on single-input systems to predict the n-dimensional induction responses of systems with n inputs. We demonstrate that this approach accurately predicts Boolean (on/off) responses of multi-input systems consisting of novel chimeric transcription factors and hybrid promoters in Escherichia coli. The second method uses only a small amount of multi-input response data to accurately predict analog system response over the entire landscape of input combinations. Taken together, these methods facilitate the design of synthetic circuits that utilize multi-input promoters.