Orthogonality and burdens of heterologous AND gate gene circuits in E. coli

File Description SizeFormat 
accepted ms_ACS Synbio_circuit host interaction.pdf.pdfFile embargoed until 14 December 20182.35 MBAdobe PDF    Request a copy
Title: Orthogonality and burdens of heterologous AND gate gene circuits in E. coli
Author(s): Liu, Q
Schumacher, J
Wan, X
Lou, C
Wang, B
Item Type: Journal Article
Abstract: Synthetic biology approaches commonly introduce heterologous gene networks into a host to predictably program cells, with the expectation of the synthetic network being orthogonal to the host background. However, introduced circuits may interfere with the host’s physiology, either indirectly by posing a metabolic burden and/or through unintended direct interactions between parts of the circuit with those of the host, affecting functionality. Here we used RNA-Seq transcriptome analysis to quantify the interactions between a representative heterologous AND gate circuit and the host Escherichia coli under various conditions including circuit designs and plasmid copy numbers. We show that the circuit plasmid copy number outweighs circuit composition for their effect on host gene expression with medium-copy number plasmid showing more prominent interference than its low-copy number counterpart. In contrast, the circuits have a stronger influence on the host growth with a metabolic load increasing with the copy number of the circuits. Notably, we show that variation of copy number, an increase from low to medium copy, caused different types of change observed in the behaviour of components in the AND gate circuit leading to the unbalance of the two gate-inputs and thus counterintuitive output attenuation. The study demonstrates the circuit plasmid copy number is a key factor that can dramatically affect the orthogonality, burden and functionality of the heterologous circuits in the host chassis. The results provide important guide for future efforts to design orthogonal and robust gene circuits with minimal unwanted interaction and burden to their host.
Publication Date: 14-Dec-2017
Date of Acceptance: 14-Dec-2017
URI: http://hdl.handle.net/10044/1/55597
DOI: https://dx.doi.org/10.1021/acssynbio.7b00328
ISSN: 2161-5063
Publisher: American Chemical Society
Start Page: 553
End Page: 564
Journal / Book Title: ACS Synthetic Biology
Volume: 7
Issue: 2
Copyright Statement: © 2017 American Chemical Society. This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Synthetic Biology, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://dx.doi.org/10.1021/acssynbio.7b00328
Keywords: Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biochemistry & Molecular Biology
gene circuit
host circuit interaction
orthogonality
metabolic burden
RNA-Seq
synthetic biology
LOGIC GATES
RNA-SEQ
EXPRESSION
NETWORKS
CELL
PRINCIPLES
GENERATION
ALLOCATION
DATABASE
SIGNALS
RNA-Seq
gene circuit
host circuit interaction
metabolic burden
orthogonality
synthetic biology
Publication Status: Published
Embargo Date: 2018-12-14
Appears in Collections:Faculty of Natural Sciences



Items in Spiral are protected by copyright, with all rights reserved, unless otherwise indicated.

Creative Commons