Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks

Title	Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks
Authors	Enoch Yeung, Aaron J. Dy, Kyle B. Martin, Andrew H. Ng, Domitilla Del Vecchio, James L. Beck, James J. Collins and Richard M. Murray
Source	Cell Systems, 5(1):11–24.e12, 2017
Abstract	Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability.
Type	Journal paper
URL	http://www.cell.com/cell-systems/fulltext/S2405-4712(17)30229-6
DOI
Tag	yeu+17-cellsys
ID	2017e
Funding	AFOSR BRI
Flags	Biocircuits