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

J Bacteriol. 2007 Dec;189(24):8786-92. doi: 10.1128/JB.00977-07. Epub 2007 Oct 5.


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 delta fnr, delta crp, and delta 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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial / genetics
  • DNA-Binding Proteins / genetics*
  • Escherichia coli / genetics*
  • Escherichia coli / physiology
  • Escherichia coli Proteins / genetics*
  • Genome, Bacterial / genetics
  • Genomic Instability*
  • Microarray Analysis
  • Molecular Sequence Data
  • Nucleic Acid Hybridization*
  • Phenotype
  • Polymerase Chain Reaction
  • Sequence Deletion / genetics*
  • Trans-Activators / genetics*


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Trans-Activators
  • flhC protein, E coli
  • flhD protein, E coli

Associated data

  • GEO/GSE3591
  • GEO/GSE7695