Escherichia coli Raw sequence reads
This study aims to elucidate the molecular mechanisms underlying the recovery of robust growth in an engineered Escherichia coli strain utilizing ethanol as the sole carbon source for fumarate production. The parental strain Q5176 exhibits severe growth defects when cultivated with ethanol as the sole carbon source. After 180 days of adaptive laboratory evolution under ethanol selection pressure, the evolved strain Q5995 regained robust growth capability. Key genomic mutations identified by whole-genome resequencing were subsequently reconstituted in the parental background to generate the engineered strain Q6593. To comprehensively characterize the transcriptional reprogramming underlying this metabolic adaptation, we performed transcriptome sequencing (RNA-seq) of the parental strain Q5176, the evolved strain Q5995, and the engineered strain Q6593 under ethanol-exclusive conditions. Comparative transcriptomic analysis will reveal genome-wide expression changes associated with the restoration of growth on ethanol, providing insights into the rewiring of central carbon metabolism, including the activation of the glyoxylate shunt and gluconeogenic pathways, following the disruption of the TCA cycle. This study establishes a framework for understanding how microbial metabolism adapts to non-native carbon sources and offers valuable targets for engineering high-carbon-economy cell factories for the production of TCA cycle-derived chemicals from sustainable C2 feedstocks.