Whole-Genome Detection of Conditionally Essential and Dispensable Genes in Escherichia coli via Genetic Footprinting

  • Michael D. Scholle
  • Svetlana Y. Gerdes
Part of the Methods in Molecular Biology™ book series (MIMB, volume 416)


We present a whole-genome approach to genetic footprinting in Escherichia coli using Tn5-based transposons to determine gene essentiality. A population of cells is mutagenized and subjected to outgrowth under selective conditions. Transposon insertions in the surviving mutants are detected using nested polymerase chain reaction (PCR), agarose gel electrophoresis, and software-assisted PCR product size determination. Genomic addresses of these inserts are then mapped onto the E. coli genome sequence based on the PCR product lengths and the addresses of the corresponding genome-specific primers. Gene essentiality conclusions were drawn based on a semiautomatic analysis of the number and relative positions of inserts retained within each gene after selective outgrowth.

Key Words

dispensable genes E. coli essential genes genetic footprinting genome Tn5 transposome transposon mapping transposon mutagenesis 


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Copyright information

© Humana Press Inc., a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Michael D. Scholle
    • 1
  • Svetlana Y. Gerdes
    • 2
  1. 1.Amunix Inc.Mountain View
  2. 2.Fellowship for Interpretation of Genomes (FIG)Burr Ridge

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