DEG analysis according to NarQ overexrpession in E. coli W WT, E. coli W NarQXLP deleted strain

ABSTRACT: In microbial biochemical production, the intracellular accumulation of target chemicals often reduces growth and productivity. One effective strategy to mitigate this problem is to minimize product reuptake. However, the application of this approach in strain development has been challenged by the limited understanding of import-related genes, especially for non-native products. Here, we developed a workflow to identify genes involved in the import of 3-hydroxypropionic acid (3-HP). We constructed a genome-wide overexpression library and coupled it with a 3-HP–responsive biosensor that converts intracellular 3-HP into fluorescence, enabling high-throughput cell sorting by flow cytometry. Sorted cells exhibited a 3.0-fold increase in fluorescence, which was attributed to the overexpression of narQ. Further analysis revealed that the histidine kinase activity of NarQ was essential for this phenotype, and NarQ enhanced import even in the absence of the canonical Nar two-component system. Transcriptome profiling under NarQ overexpression revealed a distinct set of membrane-associated genes—including acrD, mliC, and pgaABCD—that were transcriptionally upregulated as part of the NarQ regulatory response. Functional tests confirmed that overexpression of these genes enhanced 3-HP import, while their deletion in producing strains increased 3-HP titers by up to 21% compared with the control strain. Together, these results establish NarQ as a regulator of a broader membrane-associated network that indirectly governs 3-HP reuptake. This study also provides a systematic framework for identifying import-related genes directly from genomic DNA, thereby advancing the development of more efficient microbial production platforms.

ORGANISM(S): Escherichia coli

PROVIDER: GSE313402 | GEO | 2026/04/29

REPOSITORIES: GEO