Phenotypic Screening of Escherichia coli K-12 Tn 5 Insertion Libraries, Using Whole-Genome Oligonucleotide Microarrays

Abstract

ABSTRACT Complete genome sequences in combination with global screening methods allow parallel analysis of multiple mutant loci to determine the requirement for specific genes in different environments. In this paper we describe a high-definition microarray approach for investigating the growth effects of Tn 5 insertions in Escherichia coli K-12. Libraries of insertion mutants generated by a unique Tn 5 mutagenesis system were grown competitively in defined media. Biotin-labeled runoff RNA transcripts were generated in vitro from transposon insertions in each population of mutants. These transcripts were then hybridized to custom-designed oligonucleotide microarrays to detect the presence of each mutant in the population. By using this approach, the signal associated with 25 auxotrophic insertions in a 50-mutant pool was not detectable following nine generations of growth in glucose M9 minimal medium. It was found that individual insertion sites could be mapped to within 50 bp of their genomic locations, and 340 dispensable regions in the E. coli chromosome were identified. Tn 5 insertions were detected in 15 genes for which no previous insertions have been reported. Other applications of this method are discussed.