Validation of bacterial replication termination models using simulation of genomic mutations

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

In bacterial circular chromosomes and most plasmids, the replication is known to be terminated when either of the following occurs: the forks progressing in opposite directions meet at the distal end of the chromosome or the replication forks become trapped by Tus proteins bound to Ter sites. Most bacterial genomes have various polarities in their genomic structures. The most notable feature is polar genomic compositional asymmetry of the bases G and C in the leading and lagging strands, called GC skew. This asymmetry is caused by replication-associated mutation bias, and this "footprint" of the replication machinery suggests that, in contrast to the two known mechanisms, replication termination occurs near the chromosome dimer resolution site dif. To understand this difference between the known replication machinery and genomic compositional bias, we undertook a simulation study of genomic mutations, and we report here how different replication termination models contribute to the generation of replication-related genomic compositional asymmetry. Contrary to naive expectations, our results show that a single finite termination site at dif or at the GC skew shift point is not sufficient to reconstruct the genomic compositional bias as observed in published sequences. The results also show that the known replication mechanisms are sufficient to explain the position of the GC skew shift point.

Original languageEnglish
Article numbere34526
JournalPLoS One
Volume7
Issue number4
DOIs
Publication statusPublished - 2012 Apr 3

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Chromosomes
simulation models
Bacterial Chromosomes
Bacterial Genomes
mutation
genomics
Mutation
Machinery
Plasmids
chromosomes
Dimers
Genes
Proteins
plasmids
genome
Direction compound
proteins

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Validation of bacterial replication termination models using simulation of genomic mutations. / Kono, Nobuaki; Arakawa, Kazuharu; Tomita, Masaru.

In: PLoS One, Vol. 7, No. 4, e34526, 03.04.2012.

Research output: Contribution to journalArticle

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