Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes

ABSTRACT Insertion Sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of the target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element, as well as a short duplication at the target site. It has been noted that, when observing extant IS element copies in a genome, occasionally no Target Site Duplication (TSD) is readily identifiable. This has been attributed to degeneration of the TSD at some point after the insertion event. Here, we provide evidence that some IS movement events – namely, those that occur in association with large-scale genome rearrangements – occur without generating TSDs. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25, and an IS5/IS1182 movement plus a large deletion in Escherichia coli C. Additionally, we use sequencing data from the Lenski long-term evolution experiment to provide a further 14 examples of IS150 movements in E. coli B that are associated with large deletions and do not carry TSDs. Overall, our results indicate that some IS elements can insert into, and thus repair, existing DNA breaks in bacterial genomes. REPOSITORY CONTENTS This entry contains additional raw data and background information for the manuscript entitled: Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes 01_SBW25_Dup_IS: contains the background files for work on the SBW25-Dup-IS strain, including: - electrophoresis gel images - genome sequencing data and analysis files - junction sequence files and Sanger sequencing traces - stability test R code and output 02_Ec_Del_IS: contains the background files for work on the Ec-Del-IS strain, including: - electrophoresis gel images - genome sequencing data and analysis files - junction sequence files and Sanger sequencing traces 03_LTEE: contains the background files for work on 3x LTEE populations (at 60,000 generations), including: - raw sequencing reads (downloaded from NCBI BioProject database; accession number PRJNA380528) - breseq output for Ara-3, Ara-6, and Ara+1 populations - reference alignment file (NCBI RefSeq NC_012967.1)