TY - JOUR
T1 - Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli
AU - Lee, Heewook
AU - Doak, Thomas G.
AU - Popodi, Ellen
AU - Foster, Patricia L.
AU - Tang, Haixu
N1 - Funding Information:
US Army Research OfficeMultidisciplinary University Research Initiative Award [W911NF-09-1-0444 to P.L.F., in part]; National Science Foundation [DBI-1262588 to H.T.]. Funding for open access charge: US Army Research OfficeMultidisciplinary University Research Initiative Award [W911NF-09-1-0444 to P.L.F.].
Publisher Copyright:
© 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2016/9/6
Y1 - 2016/9/6
N2 - A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10-4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10-5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186. Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5′-GGGG(N6/N7)CCCC-3′. We also detected 48 long deletions not involving IS elements.
AB - A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10-4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10-5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186. Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5′-GGGG(N6/N7)CCCC-3′. We also detected 48 long deletions not involving IS elements.
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U2 - 10.1093/nar/gkw647
DO - 10.1093/nar/gkw647
M3 - Article
C2 - 27431326
AN - SCOPUS:84988377984
SN - 0305-1048
VL - 44
SP - 7109
EP - 7119
JO - Nucleic acids research
JF - Nucleic acids research
IS - 15
ER -