We previously described a gene, lpt3, required for the addition of phosphoethanolamine (PEtn) at the 3 position on the -chain heptose (HepII) of the inner-core Neisseria meningitidis lipopolysaccharide (LPS), but it has long been recognized that the inner-core LPS of some strains possesses PEtn at the 6 position (PEtn-6) on HepII. We have now identified a gene, lpt6 (NMA0408), that is required for the addition of PEtn-6 on HepII. The lpt6 gene is located in a region previously identified as Lgt-3 and is associated with other LPS biosynthetic genes. We screened 113 strains, representing all serogroups and including disease and carriage strains, for the lpt3 and lpt6 genes and showed that 36% contained both genes, while 50% possessed lpt3 only and 12% possessed lpt6 only. The translated amino acid sequence of lpt6 has a homologue (72.5% similarity) in a product of the Haemophilus influenzae Rd genome sequence. Previous structural studies have shown that all H. influenzae strains investigated have PEtn-6 on HepII. Consistent with this, we found that, among 70 strains representing all capsular serotypes and nonencapsulated H. influenzae strains, the lpt6 homologue was invariably present. Structural analysis of LPS from H. influenzae and N. meningitidis strains where lpt6 had been insertionally inactivated revealed that PEtn-6 on HepII could not be detected. The translated amino acid sequences from the N. meningitidis and H. influenzae lpt6 genes have conserved residues across their lengths and are part of a family of proven or putative PEtn transferases present in a wide range of gram-negative bacteria.The lipopolysaccharides (LPS) of the gram-negative bacteria Neisseria meningitidis and Haemophilus influenzae lack the repeating O antigens that are characteristic of the LPS of enteric bacteria. The core LPS molecule of these bacteria is heterogeneous both within and among strains and plays a role in the commensal and pathogenic behavior of each species. N. meningitidis and H. influenzae are host-restricted bacteria found exclusively in humans. They normally reside in the nasopharynx of humans but can spread contiguously within the respiratory tract or disseminate systemically into the blood to cause serious diseases such as pneumonia, septicemia, and meningitis.N. meningitidis LPS has been classified into 12 distinct immunotypes (L1 to L12), on the basis of monoclonal antibody (MAb) reactivity (42), the basis of which has been further defined by structural analysis as detailed in the following references: L1 and L6, references 11 and 49; L2, reference 13; L3, reference 36; L4 and L7, reference 29; L5, reference 35; L9, reference 22. N. meningitidis LPS is based on a diheptose backbone, which is attached via one of two 3-deoxy-D-manno-2-octulosonic acid (Kdo) residues to the lipid A portion. Additions occur to the first heptose (HepI), and extension past the proximal glucose (Glc) residue is classed as the outer-core structure (Fig. 1). The second heptose (HepII) is invariably substituted by an N-acetylglucosamine (...