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

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.