Validation of bacterial replication termination models using simulation of genomic mutations.

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 b...

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Autores principales:	Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fa7cfb7327604e75b34ed422cb651325
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spelling	oai:doaj.org-article:fa7cfb7327604e75b34ed422cb6513252021-11-18T07:23:21ZValidation of bacterial replication termination models using simulation of genomic mutations.1932-620310.1371/journal.pone.0034526https://doaj.org/article/fa7cfb7327604e75b34ed422cb6513252012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22509315/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203In 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.Nobuaki KonoKazuharu ArakawaMasaru TomitaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e34526 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nobuaki Kono Kazuharu Arakawa Masaru Tomita Validation of bacterial replication termination models using simulation of genomic mutations.
description	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.
format	article
author	Nobuaki Kono Kazuharu Arakawa Masaru Tomita
author_facet	Nobuaki Kono Kazuharu Arakawa Masaru Tomita
author_sort	Nobuaki Kono
title	Validation of bacterial replication termination models using simulation of genomic mutations.
title_short	Validation of bacterial replication termination models using simulation of genomic mutations.
title_full	Validation of bacterial replication termination models using simulation of genomic mutations.
title_fullStr	Validation of bacterial replication termination models using simulation of genomic mutations.
title_full_unstemmed	Validation of bacterial replication termination models using simulation of genomic mutations.
title_sort	validation of bacterial replication termination models using simulation of genomic mutations.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/fa7cfb7327604e75b34ed422cb651325
work_keys_str_mv	AT nobuakikono validationofbacterialreplicationterminationmodelsusingsimulationofgenomicmutations AT kazuharuarakawa validationofbacterialreplicationterminationmodelsusingsimulationofgenomicmutations AT masarutomita validationofbacterialreplicationterminationmodelsusingsimulationofgenomicmutations
_version_	1718423573940404224

Validation of bacterial replication termination models using simulation of genomic mutations.

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