Cell-cell communication in yeast using auxin biosynthesis and auxin responsive CRISPR transcription factors

Abstract

A true engineering framework for synthetic multicellular systems requires a programmable means of cell-cell communication. Such a communication system would enable complex behaviors, such as pattern formation, division of labor in synthetic microbial communities, and improved modularity in synthetic circuits. However, it remains challenging to build synthetic cellular communication systems in eukaryotes due to a lack of molecular modules that are orthogonal to the host machinery, easy to reconfigure, and scalable. Here, we present a novel cell-to-cell communication system in Saccharomyces cerevisiae (yeast) based on CRISPR transcription factors and the plant hormone auxin that exhibits several of these features. Specifically, we engineered a sender strain of yeast that converts indole-3-acetamide (IAM) into auxin via the enzyme iaaH from Agrobacterium tumefaciens. To sense auxin and regulate transcription in a receiver strain, we engineered a reconfigurable library of auxin degradable CRISPR transcription factors (ADCTFs). Auxin-induced degradation is achieved through fusion of an auxin sensitive degron (from IAA co-repressors) to the CRISPR TF and co-expression with an auxin F-box protein. Mirroring the tunability of auxin perception in plants, our family of ADCTFs exhibits a broad range of auxin sensitivities. We characterized the kinetics and steady state behavior of the sender and receiver independently, and in co-cultures where both cell types were exposed to IAM. In the presence of IAM, auxin is produced by the sender cell and triggers de-activation of reporter expression in the receiver cell. The result is an orthogonal, rewireable, tunable, and arguably scalable cell-cell communication system for yeast and other eukaryotic cells.