RT Journal Article
SR Electronic
T1 Programming mRNA decay to modulate synthetic circuit resource allocation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 079939
DO 10.1101/079939
A1 Ophelia S. Venturelli
A1 Mika Tei
A1 Stefan Bauer
A1 Leanne Jade G. Chan
A1 Christopher J. Petzold
A1 Adam P. Arkin
YR 2016
UL http://biorxiv.org/content/early/2016/10/09/079939.abstract
AB Synthetic biomolecular networks embedded in host-cells compete with cellular processes for limited intracellular resources. Resource utilization is a major variable that impacts synthetic circuit behavior. Here we show that intracellular resources could be diverted from cellular operations to a synthetic circuit by programming global mRNA decay using the sequence-dependent endoribonuclease MazF. Synthetic circuit genes were protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and the metabolic flux of a high-value metabolite gluconate were significantly enhanced using this genome-scale control strategy. Proteomics measurements discovered a key host translation factor in need of protection to optimize the resource redistribution activity. A dynamic computational model demonstrated that the MazF mRNA-decay feedback loop achieved proportional control of MazF levels in an optimal operating regime. RNA-seq time-series measurements of MazF-induced cells elucidated the dynamic shifts in the transcript abundance and discovered regulatory design elements that could be used to expand the control mechanisms of the MazF resource allocator. Together, these results demonstrated that manipulation of resource allocation is a tunable parameter that can be used to redirect resources away from cellular processes to synthetic circuits to enhance target functions.