Investigating How Genomic Contexts Impact IS5 Transposition Within the Escherichia coli Genome

Insertions of the transposable element IS5 into its target sites in response to stressful environmental conditions, DNA structures, and DNA-binding proteins are well studied, but how the genomic contexts near IS5's native loci impact its transpositions is largely unknown. Here, by examining the roles of all 11 copies of IS5 within the genome of <i>E. coli</i> strain BW25113 in transposition, we reveal that the most significant copy of IS5 is one nested within and oriented in the same direction as the <i>nmpC</i> gene, while two other copies of IS5 harboring point mutations are hardly transposed. Transposition activity is heavily reliant on the upstream <i>nmpC</i> promoter that drives IS5 transposase gene <i>ins5A</i>, with more transpositions resulting from greater promoter activity. The IS5 element at <i>nmpC</i> but not at other loci transcribed detectable amounts of <i>ins5A</i> mRNA. By increasing expression of the <i>ins5CB</i> operon harbored in IS5, we demonstrate that Ins5B and Ins5C appear to exert a stimulatory role in IS5 transposition, suggesting that the downstream genomic regions near the native loci are involved in overall IS5 transposition as well. Using a strain that carries IS5 only at the <i>nmpC</i> locus, we confirm that IS5 primarily uses a copy/paste mechanism for transposition, although we cannot rule out the cut/paste mechanism.