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Comparative Genomic Hybridization Detects Secondary Chromosomal Deletions in Escherichia coli K-12 MG1655 Mutants and Highlights Instability in the flhDC Region

Jon L. Hobman,^1, Mala D. Patel,¹ G. Aida Hidalgo-Arroyo,¹ S. James L. Cariss,² Matthew B. Avison,² Charles W. Penn,^1* and Chrystala Constantinidou¹

School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom,¹ Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom²

Received 20 June 2007/ Accepted 25 September 2007

The use of whole-genome microarrays for monitoring mutagenized or otherwise engineered genetic derivatives is a potentially powerful tool for checking genomic integrity. Using comparative genomic hybridization of a number of unrelated, directed deletion mutants in Escherichia coli K-12 MG1655, we identified unintended secondary genomic deletions in the flhDC region in fnr, crp, and creB mutants. These deletions were confirmed by PCR and phenotypic tests. Our findings show that nonmotile progeny are found in some MG1655 directed deletion mutants, and studies on the effects of gene knockouts should be viewed with caution when the mutants have not been screened for the presence of secondary deletions or confirmed by other methods.

Published ahead of print on 5 October 2007.

Present address: School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, United Kingdom.