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 language | English |
|---|---|
| Pages (from-to) | 3110-3117 |
| Number of pages | 8 |
| Journal | Genome Biology and Evolution |
| Volume | 10 |
| Issue number | 11 |
| DOIs | |
| Publication status | Published - 2018 Nov 1 |
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ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
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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 journal › Article
}
TY - JOUR
T1 - Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli
AU - Kono, Nobuaki
AU - Tomita, Masaru
AU - Arakawa, Kazuharu
PY - 2018/11/1
Y1 - 2018/11/1
N2 - 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.
AB - 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.
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U2 - 10.1093/gbe/evy237
DO - 10.1093/gbe/evy237
M3 - Article
C2 - 30371772
AN - SCOPUS:85057529620
VL - 10
SP - 3110
EP - 3117
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
SN - 1759-6653
IS - 11
ER -