Sulfoquinovose Catabolism in E. coli Strains: Compositional and Functional Divergence of yih Gene Cassettes

Abstract

The sulfo-Embden-Meyerhof-Parnas (sulfo-EMP) pathway enables Escherichia coli to utilize sulfoquinovose, (SQ) a sulfonated sugar derived from plant sulfolipids, as a carbon source. This pathway is encoded by the yih gene cassette. However, structural and functional diversity of this cassette across E. coli strains has not been fully characterized. We identified two structural variants of the yih cassette across E. coli and Shigella strains: a long form (ompL-yihOPQRSTUVW) and a truncated short form (yihTUVW). Both forms occupy the same genomic location but differ in orientation and are scattered across the phylogenetic tree, suggesting frequent recombination events. Transcriptome analyses revealed that only the long cassette, as found in E. coli K-12 MG1655, is transcriptionally induced during growth on sulfoquinovose. The short cassette, found in E. coli Nissle 1917 and other host-adapted strains, showed no differential expression. Despite this, both strains grew comparably on sulfoquinovose, indicating different metabolic adaptation strategies. Gene expression profiling revealed shared stress responses but distinct central metabolic patterns. Electrophoretic mobility shift assays further demonstrated that the transcription factor YihW from Nissle 1917 binds its DNA targets with lower affinity than the homolog from K-12 and shows weaker sulfoquinovose-dependent dissociation.

Keywords: Escherichia coli; Nissle 1917; RNA-seq; bacterial adaptation; operon evolution; sulfoquinovose; sulfur metabolism; yih cassette.

Figure 1

Position of yih cassettes relative to UOGs: (A) Most common configuration of the long cassette, represented by E. coli K-12 MG1655; (B) Most common configuration of the short cassette, represented by E. coli Nissle 1917.

Figure 2

Phylogenetic tree of Escherichia coli and Shigella spp. Phylogroups are marked by different colors. The presence of yih genes is indicated by colored dots, revealing two distinct types: a long variant (e.g., ompLyihOPQRTSUVW in E.coli K12 MG1655) and a short variant (e.g., yihTUVW in E. coli Nissle 1917).

Figure 3

Distribution of DEGs in E. coli K-12 (A) and E. coli Nissle 1917 (B) during growth on SQ compared to growth on glucose. Upregulated genes are marked orange, downregulated genes are marked blue, genes without significant changes in expression are marked gray. The top ten DEGs are labeled. The x-axis represents log₂(fold change), the y-axis represents the −log₁₀(adjusted p-value). Thresholds for significance are indicated by violet dashed lines at log₂(fold change) = ±2 and −log₁₀(adjusted p-value) ≈ 1.3 (corresponding to an adjusted p-value of 0.05).

Figure 4

Expression of the yih cassette genes in E. coli K-12 MG1655 and E. coli Nissle 1917 after four hours of growth on D-glucose or SQ as a sole carbon source. Standard deviations were calculated based on three biological and four technical replicates.

Figure 5

Growth of E. coli K-12 MG1655 and E. coli Nissle 1917 strains in the presence of 0.2% D-glucose or SQ as sole carbon source. Mean values and 95% confidence intervals were obtained on three biological replicates.

Figure 6

Enriched KEGG pathways in E. coli K-12 MG1655 (A) and E. coli Nissle 1917 (B) grown on SQ. Gene categories with the most enriched pathways are colored based on their log₂(fold change) values, where blue indicates downregulation, orange indicates upregulation, and gray represents mid-range expression levels.

Figure 7

Binding of YihW from E. coli Nissle 1917 to the yihU/V intergenic region from E. coli Nissle 1917 and E. coli K-12 MG1655. (A) 30 °C (B) 37 °C. The YihW:DNA molar ratio, template strains, and the presence of SQ are indicated above the lanes. (C) Comparison of binding properties of YihW from E. coli Nissle 1917 and YihW (CsqR) from E. coli K-12 MG1655 with the yihU/V intergenic region from E. coli Nissle 1917 at 37 °C. The protein origin is indicated below the lanes.

Figure 8

Binding of YihW from E. coli Nissle 1917 to the yihV/W intergenic region from E. coli Nissle1917 and E. coli K-12 MG1655 at 30 °C. The YihW:DNA molar ratio, template strains, and the presence of SQ are indicated above the lanes.