Open AccessDesign of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling
Author(s) -
Hanni Willenbrock,
Anne Petersen,
Camilla Sekse,
Kristoffer Kiil,
Yngvild Wasteson,
David W. Ussery
Publication year - 2006
Publication title -
journal of bacteriology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.652
H-Index - 246
eISSN - 1067-8832
pISSN - 0021-9193
DOI - 10.1128/jb.01043-06
Subject(s) - biology , escherichia coli , genome , computational biology , genetics , microarray , profiling (computer programming) , gene expression profiling , gene , gene expression , computer science , operating system
We describe the design and evaluate the use of a high-density oligonucleotide microarray covering seven sequencedEscherichia coli genomes in addition to several sequencedE. coli plasmids, bacteriophages, pathogenicity islands, and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 (Δstx 2 ::cat ) as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labeled genomic DNA to query the microarrays and subsequently analyze common virulence genes and phage elements and perform whole-genome comparisons, we observed that O175:H16 D1 is a K-12-like strain and confirmed that its φ3538 (Δstx 2 ::cat ) phage element originated from theE. coli 3538 (Δstx 2 ::cat ) strain, with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains, providing a likely explanation for their capability to transfer φ3538 (Δstx 2 ::cat ) between them. Analyses of control samples demonstrated that results using our custom-designed microarray were representative of the true biology, e.g., by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7% of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis.