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| Search | coliBLAST | Genome Browser | Fragment Viewer | About coliBASE |
- Links to databases
- coliBASE schema
- Type III Secretion System genes in E. coli K12
Links to databases
| coliBASE | Comparative Genomics of E. coli, Shigella and Salmonella | http://colibase.bham.ac.uk |
| CampyDB | Comparative Genomics of Campylobacter spp. | http://campy.bham.ac.uk |
| ClostriDB | Comparative Genomics of Clostridium spp. | http://clostri.bham.ac.uk |
| ViruloGenome | BLAST against the predicted protein products from unfinished genome sequence projects | http://www.vge.ac.uk |
| The E. coli Index | General information on E. coli as a model organism and a pathogen | http://ecoli.bham.ac.uk |
coliBASE Schema
A simplified representation of the coliBASE relational database schema is shown below. In the real database the Alignment table is separated into individual tables for each pairwise alignment, to minimise the database access time. Similarly, data from the cds and swissprot tables are consolidated into an additional annotation table to improve the response speed of the initial search page. The schema is generic, and can be applied to other bacterial species (as has already been done for Campylobacter and Clostridium).
Type III Secretion System genes in E. coli K12
Previous authors have noted the existence of K12 homologues of genes from the Spi-1 and Spi-3 pathogenicity islands from Salmonella enterica, and in particular remarked on the presence in this commensal strain of genes usually associated with type III secretion (Hueck, 1998; Blanc-Potard et al., 1999). Why these genes occur in K12 remains a mystery until genomic comparisons with several pathogenic strains are performed.
One of the novel features revealed by the complete genome sequencing of enterohaemorrhagic E. coli O157:H7 (Hayashi et al., 2001; Perna et al., 2001) was the presence of a second type three secretion system (TTSS), which was named ETT2 (E. coli Type Three secretion system 2). ETT2 is present in O-island 122, a region of the O157 genome that appears to be an insertion relative to the K12 genome. O-island 122 and its flanking regions from the E. coli O157:H7 Sakai strain are shown below, aligned to the equivalent regions from E. coli K12 MG1655 (this image was generated using the coliBASE Alignment Viewer). Inspection of the genes flanking O-island 122 shows the presence of genes that, although present in both O157 and K12, are homologues of known TTSS genes. For example the gene ygeH (ECs3709) is a homologue of the Salmonella typhimurium TTSS regulator gene hilA, and is annotated as encoding a putative invasion protein.
View this alignment in coliBASE