Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks
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Collins-CELL-SYSTEMS.pdf
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Author(s)
Yeung, Enoch
Martin, Kyle B.
Ng, Andrew H.
Beck, James L.
Murray, Richard M.
Dy, Aaron James
Del Vecchio, Domitilla
Collins, James J.
Date Issued
July 2017
Journal
Cell Systems
Publisher
Elsevier BV
Citation
Yeung, Enoch, Aaron J. Dy, Kyle B. Martin, Andrew H. Ng, Domitilla Del Vecchio, James L. Beck, James J. Collins, and Richard M. Murray. “Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks.” Cell Systems 5, no. 1 (July 2017): 11–24.e12.
Version
Original manuscript
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.
MIT Department
Institute for Medical Engineering and Science
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Mechanical Engineering
Massachusetts Institute of Technology. Plasma Science and Fusion Center
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Creative Commons Attribution-NonCommercial-NoDerivs License
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DOI of Published Version
https://doi.org/10.1016/J.CELS.2017.06.001
