Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

• Published in: Cell 2023-08, Vol.186 (18), p.3810-3825.e18
• Main Authors: Bragdon, Meghan D.J., Patel, Nikit, Chuang, James, Levien, Ethan, Bashor, Caleb J., Khalil, Ahmad S.
• Format: Article
• Language: English
• Subjects: cooperativity; DNA; fitness; gene circuits; gene regulation; Gene Regulatory Networks; Genome; modeling; Saccharomyces cerevisiae - genetics; specificity; synthetic biology; synthetic genes; transcription (genetics); transcription factor; Transcription Factors - genetics; yeast; yeasts; zinc fingers
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2023.07.012

A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits “wired” using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications. [Display omitted] •Circuits that utilize artificial zinc-finger TFs impose a fitness burden in yeast•Wiring circuits using cooperative assembly of weakly binding TFs restores fitness•TF assembly enhances specificity and reduces off-target misregulation of transcription•Circuits with cooperative TF assemblies show genetic stability in long-term culture Circuits composed of artificial zinc-finger transcriptional regulators establish cooperative assembly as a mechanism for achieving regulatory specificity and allow for construction of robust gene circuits scalable to a wide range of host organisms and applications.