Untargeted metabolomics analysis of Ralstonia eutropha during plant oil cultivations reveals the presence of a fucose salvage pathway

Björn Gutschmann,Sebastian L. Riedel,Martina C. E. Bock,Stefan Jahns,Christopher J. Brigham,Peter Neubauer

doi:10.1038/s41598-021-93720-9

Björn Gutschmann, Sebastian L. Riedel + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-93720-9

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Abstract

Process engineering of biotechnological productions can benefit greatly from comprehensive analysis of microbial physiology and metabolism. Ralstonia eutropha (syn. Cupriavidus necator) is one of the best studied organisms for the synthesis of biodegradable polyhydroxyalkanoate (PHA). A comprehensive metabolomic study during bioreactor cultivations with the wild-type (H16) and an engineered (Re2058/pCB113) R. eutropha strain for short- and or medium-chain-length PHA synthesis has been carried out. PHA production from plant oil was triggered through nitrogen limitation. Sample quenching allowed to conserve the metabolic states of the cells for subsequent untargeted metabolomic analysis, which consisted of GC–MS and LC–MS analysis. Multivariate data analysis resulted in identification of significant changes in concentrations of oxidative stress-related metabolites and a subsequent accumulation of antioxidative compounds. Moreover, metabolites involved in the de novo synthesis of GDP-l-fucose as well as the fucose salvage pathway were identified. The related formation of fucose-containing exopolysaccharides potentially supports the emulsion-based growth of R. eutropha on plant oils.

Highlights

Process engineering of biotechnological productions can benefit greatly from comprehensive analysis of microbial physiology and metabolism
R. eutropha H16 and the engineered strain R. eutropha Re2058/pCB113 were grown in biological triplicate bioreactor cultivations to perform non-targeted metabolite analysis under controlled conditions for a further elucidation of the metabolic activities during growth and PHA formation under nitrogen limitation on plant oils
The cultivation of the wild-type strain yielded in a final cell dry weight (CDW) of 27.8 g L−1 with a polyhydroxybutyrate (PHB) content of 62 wt% (17.2 gPHB L−1)

Summary

Introduction

Process engineering of biotechnological productions can benefit greatly from comprehensive analysis of microbial physiology and metabolism. A comprehensive metabolomic study during bioreactor cultivations with the wild-type (H16) and an engineered (Re2058/pCB113) R. eutropha strain for short- and or medium-chain-length PHA synthesis has been carried out. The metabolic characteristics of R. eutropha H16, a scl-PHA producer, and Re2058/pCB113, a scl-co-mcl-PHA producer, were examined during bioreactor cultivations under growth and nitrogen limitation (PHA synthesis) conditions using plant oil as the main carbon source. Both strains were evaluated by nontargeted metabolite profiling. The metabolite profiling yielded the identification of the de novo and salvage pathway synthesis of GDP-l-fucose, a component of exopolysaccharide/lipopolysaccharide (EPS/LPS), as well as oxidative stressrelated metabolite changes

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