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Series GSE8889 Query DataSets for GSE8889
Status Public on Apr 01, 2008
Title Genomic Comparison of the O-antigen Biosynthesis Gene Clusters of E. coli O55 Strains Belonging to Three Lineages.
Organism Escherichia coli
Experiment type Genome variation profiling by array
Summary Typical enteropathogenic Escherichia coli (EPEC) O55:H7 is regarded as the closest relative of enterohemorrhagic E. coli (EHEC) O157:H7. Both serotypes usually express the γ1 intimin subclass and trigger actin polymerazation by the Tir-TccP pathway. However, atypical O55:H7 strains capable of triggering actin polymerization via the Tir-Nck pathway have recently been identified. In this study, we investigated the genotypic differences and phylogenetic relationships between typical and atypical O55:H7 strains. We show that the atypical O55:H7 strains, which express the θ intimin subclass and lack both tccP and tccP2, belong to an E. coli lineage distinct from the typical O55:H7 and from the EPEC O55:H6, which also uses the Tir-Nck actin polymerization pathway. We conducted genomic comparisons of the chromosomal regions covering the O-antigen gene cluster and its flanking regions between the three O55 lineages by restriction fragment length polymorphism analysis of PCR products and DNA sequencing analysis of about 65-kb chromosomal regions. This unexpectedly revealed that horizontal transfer of large fragments (≥ 40 kb) encoding the O55-antigen gene cluster and part of neighboring colanic acid gene cluster is involved in the emergence of the three O55 E. coli lineages. The data provide new insights into the mechanisms involved in the generation of a wide variety of O-serotypes in Gram-negative bacteria.
Keywords: comparative genomic hybridization
Overall design Total 8 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) Iguchi A, Hayashi T
Citation(s) 18227260
Submission date Aug 28, 2007
Last update date Mar 17, 2012
Contact name Atsushi Iguchi
Organization name Miyazaki university
Street address Oaza-kihara 5220
City Kiyotake
ZIP/Postal code 889-1692
Country Japan
Platforms (1)
GPL5329 E. coli O157 Sakai oligonucleotide DNA microarray
Samples (16)
GSM225251 O55:H7 TB182A replicate 1
GSM225252 O55:H7 TB182A replicate 2
GSM225253 O55:H7 st957 replicate 1
BioProject PRJNA102271

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Supplementary file Size Download File type/resource
GSE8889_RAW.tar 6.0 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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