Skip Navigation


MBE Advance Access originally published online on July 23, 2007
Molecular Biology and Evolution 2007 24(10):2169-2179; doi:10.1093/molbev/msm148
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
24/10/2169    most recent
msm148v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Necsulea, A.
Right arrow Articles by Lobry, J. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Necsulea, A.
Right arrow Articles by Lobry, J. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

Anamaria Necsulea and Jean R. Lobry

Université de Lyon; université Lyon 1; CNRS; UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne F-69622, France; and HELIX, Unité de recherche INRIA

E-mail: necsulea{at}biomserv.univ-lyon1.fr.

Accepted for publication July 3, 2007.

DNA base composition asymmetry is at the basis of numerous in silico methods for the detection of the origin and terminus of replication in prokaryotes. However, most of these methods are unable to identify the evolutionary mechanisms that cause the base composition asymmetry. In prokaryotic chromosomes, due to the tendency for coorientation between replication and transcription, compositional biases that discriminate the leading strand from the lagging strand can be produced by 2 superposing mechanisms: replication-associated mutation bias and coding sequence–associated bias (such as transcription-related mutational processes or selective pressures on codon usage). We propose here a new method for the analysis of nucleotide composition asymmetry that allows the decoupling of replication-related and coding sequence–related mechanisms. This method is inspired by a recent work (Nikolaou and Almirantis 2005) that proposed an artificial chromosomal rearrangement meant to create a perfect gene orientation bias. We show that the study of nucleotide skews on the artificially rearranged chromosomes is a powerful means to assess the contributions of the 2 types of mechanisms in generating the base composition asymmetry. We applied our method to all completely sequenced prokaryotic chromosomes available. Our results confirm that in most species the replication mechanism has an important effect on base composition asymmetry but also that it has different impacts on GC and AT skews. We also analyzed the variability in AT skew direction encountered in prokaryotes. In disagreement with a recent report (Worning et al. 2006), we find that the polymerase-{alpha} subunits encoded in a genome are not sufficient to predict the sign of the AT skew on its leading strand for replication.

Key Words: DNA base composition asymmetry • origin of replication • replication-induced mutation bias • transcription orientation • bacterial genomes

Aoife McLysaght, Associate Editor


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
N. V. Sernova and M. S. Gelfand
Identification of replication origins in prokaryotic genomes
Brief Bioinform, September 1, 2008; 9(5): 376 - 391.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.