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Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations

Figure 1

Scheme of GC skew reconstruction simulation.

A: A schematic representation of the GC skew reconstruction simulation. The primary sequence was generated based on the shuffled bacterial genome sequence, which had the same base composition as the original sequence. The green and yellow triangles represent the locations of C→G mutations in the leading strand (or G→C in the lagging strand). Graphs on the right show the typical GC skew shape at each simulated time point (ti). The blue bars represent the replication termini. B: Frequency distribution of replication termini in the fork-collision model. Here, replication terminates near a locus directly opposite the origin, and the position probabilistically fluctuates according to a Gaussian distribution. The distribution was empirically derived from plasmid sequences that are likely to be terminated by fork-collision mechanisms. C: Frequency distribution of replication termini in the fork-trap model in Escherichia coli str. K-12 substr. MG1655, Escherichia coli IAI1, Proteus mirabilis HI4320. Here, replication termination occurs at Ter sites, but different Ter sites have different rates of fork arrest. D: Frequency distribution of replication terminus in the dif-stop model in Escherichia coli str. K-12 substr. MG1655. Here, all replication terminates at a single finite locus dif.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0034526.g001