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Quantification of the time-course experiments. 10 The gel presented in Fig. 1B in Grainge et al. 10 showed a time course of unlinking by XerCD-dif-FtsK50C at 25 o C of newly replicated plasmids containing dif sites. Line scans of the gel were previously published. 7 In this figure each topological class is shown as a separate series of points with linear interpolation. The caption assumes the bands observed correspond to the topologies expected from a substrate composed of replication links, i.e. 2m-crossing links (e.g. 2m-cats), and some of the corresponding knotted intermediates (open circle or 0 1 ,3 1 , 5 1 ). "Unlink" corresponds to the two unlinked components in monomeric state (topology type 0 2 1 ), and "Unknot" corresponds to the dimeric unknot (0 1 ). The quantification clearly illustrates the reduction of replication links by XerCD-FtsK site-specific recombination at dif sites. The complexity of the data is also evident, with the relative proportions of all the different topologies fluctuating from one step to the next, thus obscuring the signal.
Source publication
In Escherichia coli DNA replication yields interlinked chromosomes. Controlling topological changes associated with replication and returning the newly replicated chromosomes to an unlinked monomeric state is essential to cell survival. In the absence of the topoisomerase topoIV, the site-specific recombination complex XerCD- dif -FtsK can remove r...
Contexts in source publication
Context 1
... unlinking by XerCD-FtsK of newly replicated plasmids containing dif sites was shown in. 10 Quantification of these data gave weak justification to the assumption of stepwise reduction in complex-92 ity during the unlinking reaction. 7 As can be seen in Fig. 2, the gel quantification clearly illustrates 93 the reduction of replication links by XerCD-FtsK site-specific recombination at dif sites. However, 94 because of the complexity of the data, in order to confirm stepwise reduction one would need to repeat 95 the time course experiments 10 for each individual topology. This motivates the ...
Context 2
... the experimental data 10 only gives weak support to the assumption that the complexity goes 160 strictly down at each step of the reaction (Fig. 2 Figure 4: The substrate at the top left corner is the link 6 2 1 with two reconnection sites in parallel orientation. The pathways are represented as an oriented graph where the nodes are the knot or link types, and two nodes are connected by an edge if one can go from one to the other via a reconnection event. The substrate and ...
