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Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing.

P V Phaneuf1, S H Kim1, K Rychel2

  • 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark.

ACS Synthetic Biology
|June 27, 2024
PubMed
Summary
This summary is machine-generated.

This study used meta-analysis to find mutations improving microbial strain resilience to reactive oxygen species (ROS) stress. Identified mutations in oxyR, fur, iscR, and ygfZ enhance tolerance and reduce cellular stress responses for biomanufacturing.

Keywords:
ALE mutationsSOS responseacid stressiModulonsmeta-analysis driven strain designreactive oxygen species

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Area of Science:

  • Synthetic Biology
  • Microbial Strain Engineering
  • Genomics and Multi-omics

Background:

  • Reactive oxygen species (ROS) stress negatively impacts microbial strain performance during cultivation.
  • Strain robustness to ROS is crucial for large-scale biomanufacturing and linked to SOS response and pH tolerance.
  • Adaptive laboratory evolution (ALE) generates mutations that can improve strain characteristics.

Purpose of the Study:

  • To identify specific gene mutations that enhance microbial tolerance to reactive oxygen species (ROS) stress.
  • To leverage a meta-analysis of extensive experimental data for data-driven strain engineering.
  • To improve the robustness of an industrially important melatonin production strain.

Main Methods:

  • Integrated over 7000 adaptive laboratory evolution (ALE) mutations from 59 experiments.
  • Performed statistical association analysis between mutated genes and ROS tolerance conditions.
  • Combined mutation data with transcriptomics from 46 iModulon experiments to select mutations for reintroduction.

Main Results:

  • Significantly associated mutations in oxyR, fur, iscR, and ygfZ were identified.
  • Reintroduction of these mutations enhanced tolerance to hydrogen peroxide (H2O2) and acid stress.
  • Reduced SOS response was observed in strains with reintroduced mutations, indicating improved ROS resilience.

Conclusions:

  • Meta-analysis of multi-omics data effectively identifies mutations conferring industrially relevant phenotypes.
  • Engineered strains with specific mutations show improved tolerance to ROS and related stresses.
  • This data-driven approach optimizes microbial cell factories for biomanufacturing applications.