Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli

Research output: Contribution to journalArticle

Abstract

Most bacterial genomes display contrasting strand asymmetry in a variety of features, such as nucleotide composition and gene orientation, of the two replichores separated by the replication origin and terminus. The cause for the polarization is often attributed to mutations arising from the asymmetric replication machinery. Notably, a base compositional bias known as a GC skew is focused on as a footprint of the bacterial genome evolution driven by DNA replication. Previously, although a replication driven mutation pattern responsible for the GC skew formation or the related mathematical models have been well reported, an exact impact of the replication-related elements on the genomic structure is yet actively debated, and not confirmed experimentally. However, the GC skew formation is very time consuming and challenging in the laboratory. We, therefore, used cytosine deaminase as a DNA mutator, and by monitoring the mutations during an accelerated laboratory evolution procedure with Illumina sequencing, we enabled the trial and error of the GC skew formation in high resolution. Using this technology, we succeeded in reconfirming the influence of bacterial replication machinery on the genomic structure at high resolution.

Original languageEnglish
Pages (from-to)3110-3117
Number of pages8
JournalGenome Biology and Evolution
Volume10
Issue number11
DOIs
Publication statusPublished - 2018 Nov 1

Fingerprint

Bacterial Genomes
mutation
Escherichia coli
machinery
Mutation
genomics
cytosine deaminase
genome
Cytosine Deaminase
replication origin
DNA
Replication Origin
DNA replication
DNA Replication
footprint
asymmetry
Theoretical Models
mathematical models
Nucleotides
polarization

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli. / Kono, Nobuaki; Tomita, Masaru; Arakawa, Kazuharu.

In: Genome Biology and Evolution, Vol. 10, No. 11, 01.11.2018, p. 3110-3117.

Research output: Contribution to journalArticle

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