In bacteria with circular chromosomes, homologous recombination events can lead to the formation of chromosome dimers. In Escherichia coli, chromosome dimers are resolved by the addition of a crossover by two tyrosine recombinases, XerC and XerD, at a specific site on the chromosome, dif. Recombination depends on a direct contact between XerD and a cell division protein, FtsK, which functions as a hexameric double stranded DNA translocase. Here, we have investigated how the structure and composition of DNA interferes with Xer recombination activation by FtsK. XerC and XerD each cleave a specific strand on dif, the top and bottom strand, respectively. We found that the integrity and nature of eight bottom-strand nucleotides and three top-strand nucleotides immediately adjacent to the XerD-binding site of dif are crucial for recombination. These nucleotides are probably not implicated in FtsK translocation since FtsK could translocate on single stranded DNA in both the 5'-3' and 3'-5' orientation along a few nucleotides. We propose that they are required to stabilize FtsK in the vicinity of dif for recombination to occur because the FtsK-XerD interaction is too transient or too weak in itself to allow for XerD catalysis.
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"010 ] . However , recombination activation by FtsKγ attached to the FtsKαβ motor domain requires more than the simple FtsKγ - XerD interaction . FtsK appears to engage a special interaction with the DNA when encountering a XerCD / dif complex , suggest - ing a structural transition of the FtsK / DNA complex at the time of recombination induction [ Bonne et al . , 2009 ] ."
"We however ruled out this possibility by showing that the FtsKATP- protein, which contains an intact FtsKγ subdomain but is unable to translocate DNA, did not induce recombination in any region of the chromosome. Consistent with this observation, purified FtsKC activates XerCD/dif recombination in vitro only in the presence of ATP and if one of the dif-carrying DNA substrates is long enough for FtsK to bind to it and translocate , , , . It follows that although FtsKγ alone can induce recombination, its activity is restricted to translocating FtsK hexamers when linked to the FtsKαβ motor. "
[Show abstract][Hide abstract] ABSTRACT: The FtsK DNA-translocase controls the last steps of chromosome segregation in E. coli. It translocates sister chromosomes using the KOPS DNA motifs to orient its activity, and controls the resolution of dimeric forms of sister chromosomes by XerCD-mediated recombination at the dif site and their decatenation by TopoIV.
We have used XerCD/dif recombination as a genetic trap to probe the interaction of FtsK with loci located in different regions of the chromosome. This assay revealed that the activity of FtsK is restricted to a ∼400 kb terminal region of the chromosome around the natural position of the dif site. Preferential interaction with this region required the tethering of FtsK to the division septum via its N-terminal domain as well as its translocation activity. However, the KOPS-recognition activity of FtsK was not required. Displacement of replication termination outside the FtsK high activity region had no effect on FtsK activity and deletion of a part of this region was not compensated by its extension to neighbouring regions. By observing the fate of fluorescent-tagged loci of the ter region, we found that segregation of the FtsK high activity region is delayed compared to that of its adjacent regions.
Our results show that a restricted terminal region of the chromosome is specifically dedicated to the last steps of chromosome segregation and to their coupling with cell division by FtsK.
PLoS ONE 07/2011; 6(7):e22164. DOI:10.1371/journal.pone.0022164 · 3.23 Impact Factor
"FtsK moves along the chromosome unidirectionally towards the dif sequence, thanks to polar and orientated sequences, the KOPS [11-13]. CDR is initiated when FtsK reaches dif and its extreme C-terminal domain directly interacts with the C-terminal domain of XerD [14-18]. The dif/XerCD chromosome dimer resolution system seems widely conserved. "
[Show abstract][Hide abstract] ABSTRACT: 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.
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.
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.