YfiM is a lipid-linked oligosaccharide pyrophosphatase
Lipid-linked oligosaccharides (LLO), such as Lipid II and O-antigen precursors in bacteria, and dolichol-linked oligosaccharides (DLO) in eukaryotes, are universal metabolic intermediates required for cell wall assembly and protein glycosylation across all domains of life. The oligosaccharide moiety of LLO is synthesized through the sequential addition of various monosaccharides, a process catalyzed by a series of glycosyltransferases, to form the final mature structure. However, the existence of a homeostasis and quality control mechanism to degrade surplus and aberrant LLO has long remained a mystery. Although we recently identified the yeast LLP1 as an LLO pyrophosphatase involved in the homeostasis and quality control of DLO in fungi, the corresponding mechanism in bacteria and plants has remained elusive. Here, we identify YfiM and AT1G15900 as LLO pyrophosphatases in Escherichia coli and Arabidopsis thaliana, respectively. Phylogenetic profiling revealed that while YfiM is broadly conserved among Gram-negative bacilli, its plant ortholog displays a unique lineage-specific distribution shaped by selective gene loss. In vitro, purified YfiM and AT1G15900 exhibit LLO pyrophosphatase activity. In vivo, deletion mutant of yfiM caused vancomycin sensitivity in E. coli. Conversely, overexpression of YfiM triggered osmotic lysis under hypotonic conditions. Moreover, overexpression of YfiM in an outer membrane-compromised strain partially rescued detergent-chelator sensitivity, revealing a compensatory envelope stress response. Together, our findings uncover an ancient, conserved cross-kingdom system for LLO quality control bridging prokaryotes and plants.