Synthetic Biology in the Alkaliphile Planctomyces limnophilus
A wiring diagram showing the general architecture of the Yeung lab regression autoencoder architecture. Promoter sequences are ingested on the left and reconstructed on the right to compute a reconstruction loss, while simultaneously regressed in the regression kernel (gray) against a phenotyical measurement, such as transcriptional activity.
The vast majority of synthetic biological parts and circuits are designed to operate in aerobic, idealized growth conditions. Genetic circuits that operate in extremely alkaline, anaerobic conditions are strikingly absent from synthetic biology despite their potential to contribute to bioremediation and biological upcycling. This study aims to address this limitation by developing a next-generation synthetic biology toolkit of genetic parts for Planctomycetes limnophilus ATCC 43296, a facultative anaerobic alkaliphile. To this end, we will engineer and characterize a suite of constitutive promoters, inducible promoters, ribosome binding sites, and synthetic terminators in the strain P. limnophilus. Our end goal will be to construct the first synthetic genetic toggle switch to operate in highly alkaline conditions.
