Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation

<p>Abstract</p> <p>Background</p> <p>The genetic code imposes a dilemma for cells. The DNA must be long enough to encode for the complexity of an organism, yet thin and flexible enough to fit within the cell. The combination of these properties greatly favors DNA collisions, which can knot and drive recombination of the DNA. Despite the well-accepted propensity of cellular DNA to collide and react with itself, it has not been established what the physiological consequences are.</p> <p>Results</p> <p>Here we analyze the effects of recombined and knotted plasmids in <it>E. coli </it>using the Hin site-specific recombination system. We show that Hin-mediated DNA knotting and recombination (i) promote replicon loss by blocking DNA replication; (ii) block gene transcription; and (iii) cause genetic rearrangements at a rate three to four orders of magnitude higher than the rate for an unknotted, unrecombined plasmid.</p> <p>Conclusion</p> <p>These results show that DNA reactivity leading to recombined and knotted DNA is potentially toxic and may help drive genetic evolution.</p

The why and how of DNA unlinking

The nucleotide sequence of DNA is the repository of hereditary information. Yet, it is now clear that the DNA itself plays an active role in regulating the ability of the cell to extract its information. Basic biological processes, including control of gene transcription, faithful DNA replication and segregation, maintenance of the genome and cellular differentiation are subject to the conformational and topological properties of DNA in addition to the regulation imparted by the sequence itself. How do these DNA features manifest such striking effects and how does the cell regulate them? In this review, we describe how misregulation of DNA topology can lead to cellular dysfunction. We then address how cells prevent these topological problems. We close with a discussion on recent theoretical advances indicating that the topological problems, themselves, can provide the cues necessary for their resolution by type-2 topoisomerases

Topoisomerase IV, alone, unknots DNA in E. coli

Knotted DNA has potentially devastating effects on cells. By using two site-specific recombination systems, we tied all biologically significant simple DNA knots in Escherichia coli. When topoisomerase IV activity was blocked, either with a drug or in a temperature-sensitive mutant, the knotted recombination intermediates accumulated whether or not gyrase was active. In contrast to its decatenation activity, which is strongly affected by DNA supercoiling, topoisomerase IV unknotted DNA independently of supercoiling. This differential supercoiling effect held true regardless of the relative sizes of the catenanes and knots. Finally, topoisomerase IV unknotted DNA equally well when DNA replication was blocked with hydroxyurea. We conclude that topoisomerase IV, not gyrase, unknots DNA and that it is able to access DNA in the cell freely. With these results, it is now possible to assign completely the topological roles of the topoisomerases in E. coli. It is clear that the topoisomerases in the cell have distinct and nonoverlapping roles. Consequently, our results suggest limitations in assigning a physiological function to a protein based upon sequence similarity or even upon in vitro biochemical activity

Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation-2

<p><b>Copyright information:</b></p><p>Taken from "Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation"</p><p>http://www.biomedcentral.com/1471-2199/8/44</p><p>BMC Molecular Biology 2007;8():44-44.</p><p>Published online 25 May 2007</p><p>PMCID:PMC1904230.</p><p></p>tral axis of the double helix). In the roadblock model, the knot (or possibly Hin bound to or cleaving DNA) is impassable and stalls polymerase. Alternatively, in the breakage model, knots may break DNA as a result of forces on the plasmid