The cryptic ushA gene (ushA(c)) in natural isolates of Salmonella enterica (serotype Typhimurium) has been inactivated by a single missense mutation.

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 UshA(c) has hitherto not been known. Sequence analysis of Salmonella ushA(+) and ushA(c) alleles indicated that the relative inactivity of UshA(c) 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 UshA(c) 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.

The aprX-lipA operon of Pseudomonas fluorescens B52: a molecular analysis of metalloprotease and lipase production.

Extracellular protease and lipase production by psychrotrophic strains of Pseudomonas fluorescens is repressed by iron and regulated by temperature. The regulation of protease and lipase has been investigated in P. fluorescens B52. Whereas lipase production is increased below the optimum growth temperature ('low-temperature regulation'), protease production was relatively constant and only decreased above the optimum growth temperature. The genes encoding protease (aprX) and lipase (lipA) are encoded at opposite ends of a contiguous set of genes which also includes protease inhibitor, Type I secretion functions and two autotransporter proteins. Evidence is presented indicating that these genes constitute an operon, with a promoter adjacent to aprX which has been identified by S1 nuclease analysis. The regulation of aprX and lipA has been investigated at the RNA level and using lacZ fusion strains. Whereas the data are consistent with iron regulation at the transcriptional level, a lipA'-'lacZ fusion is not regulated by temperature, suggesting that temperature regulation is post-transcriptional or post-translational. The possibility of regulation at the level of mRNA decay is discussed.