Integrated genomic map from uropathogenic Escherichia coli J96.

Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratory E. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain K-12. We report an integrated physical and genetic map of the 5,120-kb J96 genome. The chromosome contains 26 NotI, 13 BlnI, and 7 I-CeuI macrorestriction sites. Macrorestriction mapping was rapidly accomplished by a novel transposon-based procedure: analysis of modified minitransposon insertions served to align the overlapping macrorestriction fragments generated by three different enzymes (each sharing a common cleavage site within the insert), thus integrating the three different digestion patterns and ordering the fragments. The resulting map, generated from a total of 54 mini-Tn10 insertions, was supplemented with auxanography and Southern analysis to indicate the positions of insertionally disrupted aminosynthetic genes and cloned virulence genes, respectively. Thus, it contains not only physical, macrorestriction landmarks but also the loci for eight housekeeping genes shared with strain K-12 and eight acknowledged urovirulence genes; the latter confirmed clustering of virulence genes at the large unique accessory chromosomal segments. The 115-kb J96 plasmid was resolved by pulsed-field gel electrophoresis in NotI digests. However, because the plasmid lacks restriction sites for the enzymes BlnI and I-CeuI, it was visualized in BlnI and I-CeuI digests only of derivatives carrying plasmid inserts artificially introducing these sites. Owing to an I-SceI site on the transposon, the plasmid could also be visualized and sized from plasmid insertion mutants after digestion with this enzyme. The insertional strains generated in construction of the integrated genomic map provide useful physical and genetic markers for further characterization of the J96 genome.

Type-specific contributions to chromosome size differences in Escherichia coli.

The Escherichia coli genome varies in size from 4.5 to 5.5 Mb. It is unclear whether this variation may be distributed finely throughout the genome or is concentrated at just a few chromosomal loci or on plasmids. Further, the functional correlates of size variation in different genome copies are largely unexplored. We carried out comparative macrorestriction mapping using rare-restriction-site alleles (made with the Tn10dRCP2 family of elements, containing the NotI, BlnI, I-CeuI, and ultra-rare-cutting I-SceI sites) among the chromosomes of laboratory E. coli K-12, newborn-sepsis-associated E. coli RS218, and uropathogenic E. coli J96. These comparisons showed just a few large accessory chromosomal segments accounting for nearly all strain-to-strain size differences. Of 10 sepsis-associated and urovirulence genes, previously isolated from the two pathogens by scoring for function, all were colocalized exclusively with one or more of the accessory chromosomal segments. The accessory chromosomal segments detected in the pathogenic strains from physical, macrorestriction comparisons may be a source of new virulence genes, not yet isolated by function.

Elevation of lymphocyte CD45 protein tyrosine phosphatase activity during mitosis.

CD45 is an abundant cell-surface protein tyrosine phosphatase (PTPase) of hematopoietic cells that mediates specific tyrosine dephosphorylation in lymphocyte Ag activation. The hypothesis that CD45 PTPase activity varies during progression through the cell cycle was examined in this study. Expression of CD45 PTPase activity was determined in pre-B lymphoma (70Z/3.12) and cytolytic T lymphocyte (CTLL-2) cell lines after fractionation by counterflow centrifugal elutriation into cell cycle-stage-enriched subpopulations. For both cell lines, CD45 PTPase activity was elevated 2- to 10-fold in late G2 + M fractions compared with the PTPase activity of asynchronous cells. FACS and SDS-PAGE analyses indicated that there was only a minor increase in CD45 protein expression during progression through the cell cycle, suggesting that increased CD45 PTPase activity was a result of increased enzymatic activity. Cyclin B expression in 70Z/3.12 cells was evaluated in elutriated subpopulations and intact cyclin B was present in all cell cycle phases from G1 to late G2 + M, disappearing in mitosis and just before those fractions containing maximum CD45 activity. This observation indicated that the peak PTPase activity of CD45 occurred in late mitosis or in cytokinesis. The elevation of CD45 PTPase activity in mitosis supports the hypothesis that CD45 has a role in phosphorylation events occurring during cell division.

Purification to apparent homogeneity by immunoaffinity chromatography and partial characterization of the GM3 ganglioside-forming enzyme, CMP-sialic acid:lactosylceramide alpha 2,3-sialyltransferase (SAT-1), from rat liver Golgi.

CMP-sialic acid:lactosylceramide alpha 2,3-sialyltransferase (SAT-1) has been purified approximately 40,000-fold to apparent homogeneity from rat liver Golgi. The enzyme was solubilized from Golgi vesicles in 5% lauryldimethylamine oxide and "partially" purified by affinity chromatography twice on CMP-hexanolamine and once on lactosylceramide aldehyde-Sepharose 4B. Final purification was achieved by immunoaffinity chromatography on M12GC7-Gel 10. The M12GC7 monoclonal antibody specifically inhibits and immunoprecipitates SAT-1 activity. Identification of the protein, with an apparent molecular weight by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of about 60,000 daltons, was confirmed by Western blot and immunodetection with M12GC7. SAT-1 specifically catalyzes the transfer of N-acetylneuraminic acid (NeuAc, sialic acid) to lactosylceramide (Gal beta 1-4Glc beta 1-O-ceramide), forming GM3 ganglioside. Studies on substrate specificity indicate that the preferred acceptors have the general structure saccharide beta 1-O-ceramide, a disaccharide being preferred to a monosaccharide. SAT-1 is a glycoprotein. The carbohydrate moieties are detected with specific lectins. Deglycosylation of SAT-1 with N-glycanase results in an increase in a 43,000-dalton band. The two-dimensional electrophoretogram of SAT-1 indicates a pI range of 5.7-6.2 for the 60,000-dalton protein.

Special considerations in the purification of the GM3 ganglioside-forming enzyme, CMP-sialic acid:lactosylceramide alpha 2-3 sialyltransferase (SAT-1): effects of protease inhibitors on rat hepatic SAT-1 activity.

Co-purification of an endogenous proteolytic activity has been proposed as the cause for the size heterogeneity of sialyltransferases. Reported herein are results on the effects of various protease inhibitors, sulfhydryl-reducing agents and antimicrobial agents on SAT-1 activity. Addition of protease inhibitors to immunoaffinity-purified rat liver SAT-1 dramatically affects its activity. All protease inhibitors examined, with the exception of PMSF, inhibited the purified enzyme. The most inhibitory were the cysteine (thiol) protease inhibitors. This effect is less spectacular when the effect of these inhibitors was studied on SAT-1 activity in Golgi-enriched microsomes, although the inhibition was greatest by the cysteine protease inhibitors. One dramatic effect, found in both cases, was the apparent activation of SAT-1 activity in the presence of beta-mercaptoethanol.

Special considerations in the purification of the GM3 ganglioside forming enzyme, CMP-sialic acid:lactosylceramide alpha 2-3 sialyltransferase (SAT-1): solubilization of SAT-1 with lauryldimethylamine oxide.

Lauryldimethylamine oxide (LDAO) was employed in the purification of the GM3 ganglioside forming enzyme, CMP-sialic acid:lactosylceramide alpha 2-3 sialyltransferase (SAT-1) (4). This detergent has advantages over the typically employed Triton detergents in the solubilization and stabilization of this sialyltransferase. Crude protein fractions solubilized from rat liver Golgi by several such detergents are very similar in composition as determined by two-dimensional gel electrophoresis. However, LDAO appears to activate and stabilize SAT-1 activity. It is possible that SAT-1 activation involves the structurally similar hydrophobic moieties and quaternary amino groups of LDAO and phosphatidylcholine.