Two pathways exist for cleavage of the carbon-phosphorus (C-P) bond of phosphonates, the C-P lyase and the phosphonatase pathways. It was previously demonstrated that Escherichia coli carries genes (named phn) only for the C-P lyase pathway and that Enterobacter aerogenes carries genes for both pathways (K.-S. Lee, W. W. Metcalf, and B. L. Wanner, J. Bacteriol. 174:2501-2510, 1992). In contrast, here it is shown that Salmonella typhimurium LT2 carries genes only for the phosphonatase pathway. Genes for the S. typhimurium phosphonatase pathway were cloned by complementation of E. coli ⌬phn mutants. Genes for these pathways were proven not to be homologous and to lie in different chromosomal regions. The S. typhimurium phn locus lies near 10 min; the E. coli phn locus lies near 93 min. The S. typhimurium phn gene cluster is about 7.2 kb in length and, on the basis of gene fusion analysis, appears to consist of two (or more) genes or operons that are divergently transcribed. Like that of the E. coli phn locus, the expression of the S. typhimurium phn locus is activated under conditions of P i limitation and is subject to Pho regulon control. This was shown both by complementation of the appropriate E. coli mutants and by the construction of S. typhimurium mutants with lesions in the phoB and pst loci, which are required for activation and inhibition of Pho regulon gene expression, respectively. Complementation studies indicate that the S. typhimurium phn locus probably includes genes both for phosphonate transport and for catalysis of C-P bond cleavage.Phosphonates (Pn) are a large class of molecules containing a direct carbon-phosphorus (C-P) bond in place of the more familiar carbon-oxygen-phosphorus bond of phosphoesters. Although Pn do not exist in all organisms, they do exist in many different ones. Pn have been found in organisms as diverse as the intracellular procaryote Bdellovibrio species, the filamentous bacteria streptomycetes, the protozoans Tetrahymena and Trypanosoma spp., mollusks, insects, and others. In these organisms, Pn have been isolated as constituents of glycolipids, glycoproteins, polysaccharides, or phosphonolipids. In Bacteroides fragilis, Pn were identified as components of capsular polysaccharide (6); in streptomycetes, Pn are synthesized as antibiotics such as fosfomycin (25); in Tetrahymena spp., Pn exist as phosphonolipids (19); in Trypanosoma cruzi, Pn are components of lipopeptidophosphoglycan (the major cell surface glycoconjugate [10]); in a sea anemone, Pn are the major P compounds (38); and in a locus, a Pn is the principal P compound of hemolymph (20). Yet, in spite of their widespread natural occurrence, the biological role of natural Pn is poorly understood (17). In phosphonolipids, 2-aminoethylphosphonate (AEPn) exists in place of its analog ethanolamine phosphate.No doubt because of the abundance of PN in nature, bacteria have acquired pathways for Pn breakdown. Bacteria capable of breaking the C-P bond may use Pn as a sole P source, for which two pathways exist, the C-P l...