Heuristic Design and Engineering of Synthetic Yeast Promoters

We present a general strategy to iteratively design and engineer synthetic promoters for Saccharomyces cerevisae inducible to environmental conditions or stresses of interest, exclusively employing yeast’s native regulatory mechanisms. Starting from available experimental data from the relevant literature, focusing on transcriptome and transcription factor binding data, we identify transcription factor binding sites (TFBS) and other elements relevant to regulation by environmental conditions of interest. Where necessary, we generated our own transcriptome data. We then used these to modify the upstream activation sequences of yeast promoters and either create or improve their regulatory response to a condition of interest. We also discuss approaches to increase and stabilize basal output, and our results in this area. We demonstrate the validity and flexibility of this approach by creating sets of strong promoters inducible by either low pH or the ionic liquid ethylmethylimidazolium (EMIM) acetate, conditions chosen for their relevance to industry. The promoters are characterized at different levels of the inducing signals over different time points and phases of growth, and in the case of low pH induction ultimately used in the production industrially relevant chemical in a yeast cell factory, outperforming under the same conditions a native, constitutive promoter commonly used in metabolic engineering. In summary, our approach provides a working solution bridging true de novo synthesis espoused by synthetic biology and the use of endogenous yeast promoters in metabolic engineering applications irrespective of their suitability for the task.