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Open Access Research article

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

Nobuaki Kono12, Kazuharu Arakawa2* and Masaru Tomita23

Author Affiliations

1 Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-8520, Japan

2 Institute for Advanced Biosciences, Keio University, Japan, Endo 5322, Fujisawa, Kanagawa 252-8520, Japan

3 Department of Environment and Information Studies, Keio University, Endo 5322, Fujisawa, Kanagawa 252-8520, Japan

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BMC Genomics 2011, 12:19  doi:10.1186/1471-2164-12-19

Published: 11 January 2011

Abstract

Background

During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, dif.

Results

To study the evolution of the dif/XerCD system and its relationship with replication termination, we report the comprehensive prediction of dif sequences in silico using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, dif sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The dif sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted dif sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures.

Conclusions

The sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between dif position and the degree of GC skew suggests that replication termination does not occur strictly at dif sites.