Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization.

The availability of bacterial genome sequences raises an important new problem - how can one move from completely sequenced microorganisms as a reference to the hundreds and thousands of other strains or isolates of the same or related species that will not be sequenced in the near future? An efficient way to approach this task is the comparison of genomes by subtractive hybridization. Recently we developed a sensitive and reproducible subtraction procedure for comparison of bacterial genomes, based on the method of suppression subtractive hybridization (SSH). In this work we demonstrate the applicability of subtractive hybridization to the comparison of the related but markedly divergent bacterial species Escherichia coli and Salmonella typhimurium. Clone libraries representing sequence differences were obtained and, in the case of completely sequenced E. coli genome, the differences were directly placed in the genome map. About 60% of the differential clones identified by SSH were present in one of the genomes under comparison and absent from the other. Additional differences in most cases represent sequences that have diverged considerably in the course of evolution. Such an approach to comparative bacterial genomics can be applied both to studies of interspecies evolution - to elucidate the "strategies" that enable different genomes to fit their ecological niches - and to development of diagnostic probes for the rapid identification of pathogenic bacterial species.

Purification and some properties of Thermotoga neapolitana thermostable xylanase B expressed in E. coli cells.

A xylanase was purified from the recombinant strain E. coli TG1 carrying the pTT32 vector with a fragment of the Thermotoga neapolitana chromosomal DNA. The enzyme was purified 419-fold with 36% yield after heating at 70 degrees C and pH 4.5 and subsequent ion-exchange chromatography. By polyacrylamide gel electrophoresis in the presence of SDS, the molecular weight of the apparently homogeneous protein is 39 kD. By isoelectric focusing, the protein is of a single form with pI = 5.9. The optimal pH for hydrolysis is 5.5, and the optimal temperature is 90 degrees C. The xylanase is stable to heating at 70 degrees C for 4 h. The enzyme is inactivated by 50% at 80, 90, and 100 degrees C after 227, 162, and 30 min, respectively. Enzyme activity was tested using xylans and glucans as substrates. By thin-layer chromatography of the xylan hydrolysis products, the enzyme was classified as an endoxylanase.