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Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains

Lookup NU author(s): Dr Yiming Huang, Professor Anil Wipat, Professor Jaume Bacardit

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2023 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals LLC. Foreign proteins are produced by introducing synthetic constructs into host bacteria for biotechnology applications. This process can cause resource competition between synthetic circuits and host cells, placing a metabolic burden on the host cells which may result in load stress and detrimental physiological changes. Consequently, the host bacteria can experience slow growth, and the synthetic system may suffer from suboptimal function. To help in the detection of bacterial load stress, we developed machine-learning strategies to select a minimal number of genes that could serve as biomarkers for the design of load stress reporters. We identified pairs of biomarkers that showed discriminative capacity to detect the load stress states induced in 41 engineered Escherichia coli strains.

Publication metadata

Author(s): Huang Y, Wipat A, Bacardit J

Publication type: Article

Publication status: Published

Journal: Biotechnology and Bioengineering

Year: 2024

Volume: 121

Issue: 1

Pages: 355-365

Print publication date: 01/01/2024

Online publication date: 09/10/2023

Acceptance date: 25/09/2023

Date deposited: 03/11/2023

ISSN (print): 0006-3592

ISSN (electronic): 1097-0290

Publisher: John Wiley and Sons Inc.

URL: https://doi.org/10.1002/bit.28567

DOI: 10.1002/bit.28567

Data Access Statement: Data used in this work can be downloaded at https://github.com/SBRG/precise2.

PubMed id: 37807718

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