Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli. (29th October 2018)

• Record Type: Journal Article
• Authors: Kono, Nobuaki; Tomita, Masaru; Arakawa, Kazuharu
• Editors: Gojobori, Takashi
• Is Part Of: Genome biology and evolution. Volume 10:Number 11(2018:Nov.)
• Page Start: 3110
• Page End: 3117
• Publication Date: 2018-10-29
• Subjects: circular chromosome -- ultra-sensitive quantification of heterogeneous mutations -- replication-directed genomic asymmetry -- genomic polarity; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evy237
• Languages: English
• ISSNs: 1759-6653

Abstract

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.