The cryptic ushA gene (ushA c) in natural isolates of Salmonella enterica (serotype Typhimurium) has been inactivated by a single missense mutation The GenBank accession numbers for the sequences determined in this work are AF188721–AF188732.

Two mutational mechanisms, both supported by experimental studies, have been proposed for the evolution of new or improved enzyme specificities in bacteria. One mechanism involves point mutation(s) in a gene conferring novel substrate specificity with partial or complete loss of the original (wild-type) activity of the encoded product. The second mechanism involves gene duplication followed by silencing (inactivation) of one of these duplicates. Some of these ‘silent genes’ may still be transcribed and translated but produce greatly reduced levels of functional protein; gene silencing, in this context, is distinct from the more common associations with bacterial partitioning sequences, and with genes which are no longer transcribed or translated. Whereas most Salmonella enterica strains are ushA +, encoding an active 5′-nucleotidase (UDP-sugar hydrolase), some natural isolates, including most genetically related strains of serotype Typhimurium, have an ushA allele (designated ushA c) which produces a protein with, comparatively, very low 5′-nucleotidase activity. Previous sequence analysis of cloned ushA c and ushA + genes from serotype Typhimurium strain LT2 and Escherichia coli, respectively, did not reveal any changes which might account for the significantly different 5′-nucleotidase activities. The mechanism responsible for this reduced activity of UshAc has hitherto not been known. Sequence analysis of Salmonella ushA + and ushA c alleles indicated that the relative inactivity of UshAc may be due to one, or more, of four amino acid substitutions. One of these changes (S139Y) is in a sequence motif that is conserved in 5′-nucleotidases across a range of diverse prokaryotic and eukaryotic species. Site-directed mutagenesis confirmed that a Tyr substitution of Ser-139 in Salmonella UshA+ was solely responsible for loss of 5′-nucleotidase activity. It is concluded that the corresponding single missense mutation is the cause of the UshAc phenotype. This is the first reported instance of gene inactivation in natural isolates of bacteria via a missense mutation. These results support a model of evolution of new enzymes involving a ‘silent gene’ which produces an inactive, or relatively inactive, product, and are also consistent with the evolution of a novel, but unknown, enzyme specificity by a single amino acid change.