A modelling framework linking resource-based stochastic translation to the optimal design of synthetic constructs
File(s)
Published version
Author(s)
Sarvari, Peter
Ingram, Duncan
Stan, Guy-Bart
Type
Journal Article
Abstract
The effect of gene expression burden on engineered cells has motivated the use of “whole-cell models” (WCMs) that use shared cellular resources to predict how unnatural gene expression affects cell growth. A common problem with many WCMs is their inability to capture translation in sufficient detail to consider the impact of ribosomal queue formation on mRNA transcripts. To address this, we have built a “stochastic cell calculator” (StoCellAtor) that combines a modified TASEP with a stochastic implementation of an existing WCM. We show how our framework can be used to link a synthetic construct’s modular design (promoter, ribosome binding site (RBS) and codon composition) to protein yield during continuous culture, with a particular focus on the effects of low-efficiency codons and their impact on ribosomal queues. Through our analysis, we recover design principles previously established in our work on burden-sensing strategies, namely that changing promoter strength is often a more efficient way to increase protein yield than RBS strength. Importantly, however, we show how these design implications can change depending on both the duration of protein expression, and on the presence of ribosomal queues.
Date Issued
2021-01-07
Date Acceptance
2020-12-31
Citation
Biology, 2021, 10 (1)
ISSN
2079-7737
Journal / Book Title
Biology
Volume
10
Issue
1
Copyright Statement
© 2020 by the authors. Li-censee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms and con-ditions of the Creative Commons At-tribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
License URL
Sponsor
Engineering & Physical Science Research Council (EPSRC)
Wellcome Trust
Royal Academy Of Engineering
Grant Number
EP/M002187/1
203953/Z/16/Z
CiET1819\5
Subjects
Science & Technology
Life Sciences & Biomedicine
Biology
Life Sciences & Biomedicine - Other Topics
synthetic biology
whole-cell model
translation
stochastic simulation
TASEP
construct design
burden
ribosomal queues
slow codon
TASEP
burden
construct design
ribosomal queues
slow codon
stochastic simulation
synthetic biology
translation
whole-cell model
06 Biological Sciences
Publication Status
Published
Article Number
ARTN 37