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Abstract
BackgroundDuring 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.ResultsTo 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.ConclusionsThe 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.
Highlights
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
We obtained unique candidate dif sequences in 715 chromosomes in 641 strains that were validated through multiple means, resulting in the largest collection of predicted dif sequences assembled to date
The dif sequence is located near the replication termination site for efficient chromosome dimer resolution (CDR), the replication termination site is suggested to be at a site other than the dif site, as was recently shown in vivo [42]
Summary
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. In Escherichia coli, chromosome dimers are resolved by two tyrosine recombinases, XerC and XerD, by the addition of a crossover at a specific 28-bp sequence called the dif site, which is located in the replication termination region of the chromosome [4,5]. Like Lactococci and Streptococci, chromosome dimer resolution is resolved by single tyrosine recombinases that act at specific dif site [25,26]. In this case, dimer resolution still depends on FtsK and dif is still located opposite the origin of replication between oriented polar sequences [27]. The dif-like sequences in phages often contain more variable central region that is longer than the canonical 6 bp [31,33,34], and the XerD binding arm is considerably degenerate [28]
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