Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

PLoS One. 2015 May 26;10(5):e0127446. doi: 10.1371/journal.pone.0127446. eCollection 2015.

Abstract

We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli K12 / genetics*
  • Genome, Bacterial / genetics*
  • Methyltransferases / deficiency
  • Methyltransferases / genetics*
  • Molecular Sequence Data

Substances

  • Methyltransferases

Associated data

  • GENBANK/CP009644
  • GENBANK/CP009789

Grant support

The funder provided support in the form of salaries for authors BA, EAR, DB, AF, and RJR, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.