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.

Abstract

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 M , 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 M 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 M 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 M 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.

Genome Expression Analysis of Nonproliferating Intracellular Salmonella enterica Serovar Typhimurium Unravels an Acid pH-Dependent PhoP-PhoQ Response Essential for Dormancy

“…3A; also see Table S2), was also included in the analysis. ushA encodes a putative UDP-sugar hydrolase/5=-nucleotidase that is present in S. enterica and Escherichia coli (54). RT-qPCR assays confirmed that the expression of mgtC, pagC, and ushA in nonproliferating intracellular bacteria was PhoP-PhoQ dependent (Fig.…”

Two genotypes of Xanthomonas oryzae pv. oryzae virulence identified in West Africa

“…These two genotypes of Xoo virulence identified by molecular typing were very identical to Xoo virulence pathotypes (Pta and Ptb) obtained using phenotypic pathotyping indicating possible linkage and correlation between phenotypic pathotyping and molecular typing of Xoo virulence (Adhikari et al, 1999;Lalitha et al, 2010). The high distinction pattern of each isolates in this study suggests possible high level of genetic variation among Xoo isolates in different host cells (Innes et al, 2001;Mongkolsuk et al, 2000). The genetic analyses revealed that Mta virulence genotype might cover about 84% of BLB population across Niger, Benin Republic, Nigeria, Burkina Faso, Mali, the Gambia and Guinea and possibly be responsible for most sporadic cultivars infestation and epidemics in these countries.…”

Diversity of Nitrile Hydratase and Amidase Enzyme Genes in Rhodococcus erythropolis Recovered from Geographically Distinct Habitats

“…Thus, cryptic genetic systems involving cycles of inactivation and reactivation represent a form of long-term gene regulation of rarely utilized functions operating at the level of bacterial populations (26). A silent gene that produces an inactive or relatively inactive product may be involved in the evolution of new enzymes or novel enzymatic specificities (34). If a certain metabolic demand is no longer required, a gene may acquire a mutation which either eliminates expression of the gene or eliminates activity of the gene product (2); in the latter case, a mutation which results in incorrect polypeptide folding is most likely.…”