Reprogramme the E. coli metabolism by engineering a functional carbon-fixation pathway

TL;DR

Scientists engineered E. coli to use atmospheric CO₂ through a carbon-fixation pathway, boosting sugar production and altering metabolism.

Contribution

A functional carbon-fixation pathway was successfully engineered in E. coli, enabling CO₂ utilization and metabolic changes.

Findings

E. coli engineered with the CBB cycle used atmospheric CO₂ and increased ribose and xylitol levels significantly.

Metabolomic analysis showed major changes in central carbon and amino acid metabolism after pathway engineering.

The engineered system provides a platform for evaluating carbon-fixation modules and metabolic bottlenecks.

Abstract

Rising atmospheric CO₂ levels and their impact on climate change have intensified the need for innovative carbon capture and fixation strategies. The Calvin-Benson-Bassham (CBB) cycle, a central metabolic pathway in all photoautotrophic organisms and many autotrophic bacteria, plays a pivotal role in global carbon assimilation but is limited by the low catalytic efficiency of Rubisco.

Here, we engineered a complete, functional CBB cycle in Escherichia coli, by heterologously expressing up to 13 genes encoding phosphoribulokinase, α-carboxysomes, and inorganic carbon pumps. This bioengineering approach allowed E. coli to utilize atmospheric CO2 and led to increased levels of sugars such as ribose (4.94-fold) and xylitol (8.94-fold). Detailed metabolomic profiling of central carbon metabolism using gas chromatography-mass spectrometry (GC-MS) demonstrated that installation of the CBB cycle has a notable impact on the metabolic landscape of E. coli, resulting in substantial alterations in central carbon and amino acid metabolism. These findings deepen our understanding of the natural biological carbon-fixation pathway and its engineering in heterotrophic hosts. Furthermore, this work provides a versatile platform for evaluating and selecting efficient carbon-fixation modules, as well as assessing metabolic bottlenecks in engineered systems.

These advances offer practical guidance for rational metabolic engineering in diverse organisms for biotechnological applications, including carbon sequestration, sustainable bioproduction, and crop improvement.

The online version contains supplementary material available at 10.1186/s13036-025-00612-x.

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