Comparative genomic hybridization detects secondary chromosomal deletions in Escherichia coli K-12 MG1655 mutants, and highlights instability in the flhDC region

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

^* To whom correspondence should be addressed. Email: C.W.Penn{at}bham.ac.uk.

	Abstract

The use of whole genome microarrays for monitoring mutagenised 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 non-motile progeny are found in some MG1655 directed deletion mutants, and studies on the effects of gene knock-outs should be viewed with caution when the mutants have not been screened for the presence of secondary deletions, or confirmed by other methods.