NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE7931 Query DataSets for GSE7931
Status Public on Aug 23, 2007
Title Genomic comparison in Enteroheamorragic E. coli O157 and non-O157 serotypes by comparative genomic hybridization.
Organism Escherichia coli
Experiment type Genome variation profiling by array
Summary Background: Enterohemorrhagic Escherichia coli (EHEC) O157 causes severe food-bone illness in humans. The chromosome of O157 consists of 4.1-Mb backbone sequences shared by benign E. coli K-12, and 1.4-Mb O157-specific sequences encoding many virulence determinants such as Shiga toxin genes (stxs) and the locus of enterocyte effacement (LEE). Non-O157 EHECs belonging to clonal lineages distinct from O157 also cause similar illness in humans. According to the parallel evolution model, they have independently acquired the major virulence determinants, stxs and LEE. However, the genomic differences between O157 and non-O157 EHECs have not yet systematically been analyzed. Results: By using the microarray and Whole Genome PCR scanning analyses, we performed a whole genome comparison of 20 EHEC strains of O26, O111, and O103 serotypes with O157. In non-O157 EHEC strains, although genome sizes were similar with or rather larger than O157 and the backbone regions were well conserved, O157-specific regions were very poorly conserved. Only around 20% of the O157-specific genes were fully conserved in each non-O157 serotype. However, the non-O157 EHECs contained a significant number of virulence genes found on prophages and plasmids in O157, and also multiple prophages similar but significantly divergent from those in O157. Conclusion: Although O157 and non-O157 EHECs have independently acquired a huge amount of serotype- or strain-specific genes by lateral gene transfer, they share an unexpectedly large number of virulence genes. Independent infections of similar but distinct bacteriophages carrying these virulence determinants appear to be involved in the parallel evolution of EHEC.
Keywords: comparative genomic hybridization, CGH
 
Overall design Total 29 test samples were analyzed. Genomic DNA from each test strain and a reference strain (O157 Sakai) were labeled with Cy3 and Cy5, respectively, and were cohybridized on a single array. Labeling and hybridization were performed twice independently.
 
Contributor(s) Ogura Y, Hayashi T
Citation(s) 17711596
Submission date May 28, 2007
Last update date Mar 17, 2012
Contact name Yoshitoshi Ogura
E-mail(s) y-ogura@med.miyazaki-u.ac.jp
Organization name University of Miyazaki
Department Frontier science reserch center
Street address Kihara 5200
City Kiyotake
State/province Miyazaki
ZIP/Postal code 889-1692
Country Japan
 
Platforms (1)
GPL5329 E. coli O157 Sakai oligonucleotide DNA microarray
Samples (56)
GSM194758 O157 no.2 (strain 980938) replicate 1
GSM194759 O157 no.2 (strain 980938) replicate 2
GSM194760 O157 no.3 (strain 980706) replicate 1
Relations
BioProject PRJNA100093

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE7931_RAW.tar 9.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap