Pseudomonas aeruginosa lipopolysaccharide (LPS) contains two glycoforms of core oligosaccharide (OS); one form is capped with O antigen through an ␣-1,3-linked L-rhamnose (L-Rha), while the other is uncapped and contains an ␣-1,6-linked L-Rha. Two genes in strain PAO1, wapR (PA5000) and migA (PA0705), encode putative glycosyltransferases associated with core biosynthesis. We propose that WapR and MigA are the rhamnosyltransferases responsible for the two linkages of L-Rha to the core. Knockout mutants with mutations in both genes were generated. The wapR mutant produced LPS lacking O antigen, and addition of wapR in trans complemented this defect. The migA mutant produced LPS with a truncated outer core and showed no reactivity to outer core-specific monoclonal antibody (MAb) 5C101. Complementation of this mutant with migA restored reactivity of the LPS to MAb 5C101. Interestingly, LPS from the complemented migA strain was not reactive to MAb 18-19 (specific for the core-plus-one O repeat). This was due to overexpression of MigA in the complemented strain that caused an increase in the proportion of the uncapped core OS, thereby decreasing the amount of the core-plus-one O repeat, indicating that MigA has a regulatory role. The structures of LPS from both mutants were elucidated using nuclear magnetic resonance spectroscopy and mass spectrometry. The capped core of the wapR mutant was found to be truncated and lacked ␣-1,3-L-Rha. In contrast, uncapped core OS from the migA mutant lacked ␣-1,6-L-Rha. These results provide evidence that WapR is the ␣-1,3-rhamnosyltransferase, while MigA is the ␣-1,6-rhamnosyltransferase.Pseudomonas aeruginosa is an important gram-negative opportunistic pathogen capable of producing virulence determinants, including secreted toxins and enzymes, as well as cell surface structures, such as adhesins, flagella, and lipopolysaccharide (LPS) (18). LPS is a glycolipid composed of three distinct regions: lipid A, core oligosaccharide, and O antigen. P. aeruginosa produces two forms of O antigen, which are the homopolymeric A band and the heteropolymeric B band (15,21). The gene clusters associated with the biosynthesis of Aband and B-band O antigen in P. aeruginosa have been well characterized (for reviews, see references 18 and 22). In contrast, relatively little is known about the biosynthesis of the core oligosaccharide (OS).The P. aeruginosa core OS, like that of other gram-negative bacteria, can be conceptually subdivided into the inner core and the outer core (Fig. 1). The inner core is highly conserved and contains two L-glycero-D-manno-heptose (Hep) residues and two 3-deoxy-D-manno-octulosonic acid (Kdo) residues; the genetics and enzymology of this region are the best understood to date (14). The outer core is composed of four D-glucose (D-Glc) residues, one L-rhamnose (L-Rha) residue, and one N-(L-alanyl)-D-galactosamine residue, and its biosynthesis is not fully understood. The structures of the core OS of several different serotypes, clinical isolates, and rough mutants of P. a...