Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome

Abstract

The genomes of Escherichia coli and Salmonella typhimurium are similar with respect to base composition, chromosome size, and the order, orientation and spacing of genes, but differ with respect to some 29 'loops', regions unique to one species. To evaluate the genetic basis for the structure and organization of the enteric bacterial genomes, we examined the gene encoding a non-specific acid phosphatase (phoN) which maps to a loop at 96 min on the S.typhimurium chromosome. We detected atypical base composition, codon usage pattern and trinucleotide frequencies. The 1.4 kb region containing phoN had an overall base composition of 43% G+C, while the G+C content at the third positions of codons in the phoN reading frame is only 39%, much lower than the Salmonella chromosome which averages 52%. Non-specific acid phosphatase activity, assayed in 14 Gram-negative species, was detected only in Morganella morganii and Providencia stuartii, organisms with low genomic G+C contents. Upstream of the phoN gene in Salmonella is a sequence with high similarity to the oriT region of incFII plasmids, suggesting that the phoN gene, and perhaps the entire loop structure, was acquired by lateral transmission in a plasmid-mediated event.