Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo.

McCulloch, Richard; Coggins, Lesley W.; Colloms, Sean D.; Sherratt, David J.

doi:10.1002/j.1460-2075.1994.tb06453.x

Cited by 74 publications

(83 citation statements)

References 55 publications

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“…The variations in length and height measurements can be attributed to spontaneous branch migration between the 320 bp of homology in the -structures (Ref. 45 and Fig. 2A).…”

Section: Resultsmentioning

confidence: 91%

Interaction of Branch Migration Translocases with the Holliday Junction-resolving Enzyme and Their Implications in Holliday Junction Resolution

Cañas

Suzuki

Marchisone

et al. 2014

Journal of Biological Chemistry

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Background: Bacillus subtilis RuvAB and RecG translocases and RecU resolvase are crucial in homologous recombination. Results: RecU interacts with RuvB and re-localizes it at a Holliday junction (HJ). RuvB stimulates RecU. RecG and RuvAB unwind HJs. Conclusion: A RecU⅐HJ⅐RuvAB complex might be formed. Significance: RecU, which interacts with RecA, may help to discriminate between RuvAB and RecG at HJs.

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“…The variations in length and height measurements can be attributed to spontaneous branch migration between the 320 bp of homology in the -structures (Ref. 45 and Fig. 2A).…”

Section: Resultsmentioning

confidence: 91%

Interaction of Branch Migration Translocases with the Holliday Junction-resolving Enzyme and Their Implications in Holliday Junction Resolution

Cañas

Suzuki

Marchisone

et al. 2014

Journal of Biological Chemistry

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“…Here, we focus on recombination at psi, since the products of recombination at cer contain a HJ. 20,21 We propose a few reasonable biological assumptions and, using tangles, we systematically find all possible topologies for the synapse and the strand-exchange mechanism, proving mathematically that under our assumptions there are only three solutions to the Xer tangle equations. Two of these solutions correspond to the two topological models (Figure 2) proposed by Colloms et al, 15 and have core sites aligned in parallel in the synaptic complex.…”

mentioning

confidence: 74%

“…20,21,32 The proposed mechanism for this recombination ( Figure 5) suggests that if PZ(0) with parallel sites, then R is one of the tangles (C1) or (K1). (0,0).…”

Section: Assumptions On Rmentioning

confidence: 99%

Tangle Analysis of Xer Recombination Reveals only Three Solutions, all Consistent with a Single Three-dimensional Topological Pathway

Vázquez

Colloms

Sumners

2005

Journal of Molecular Biology

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The product of Xer recombination at directly repeated psi sites on a circular unknotted DNA molecule is a right-hand four-noded catenane. Here, we use tangle equations to analyze the topological changes associated with Xer recombination at psi. This mathematical method allows computation of all possible topological pathways consistent with the experimental data. We give a rigorous mathematical proof that, under reasonable biological assumptions, there are only three solutions to the tangle equations. One of the solutions corresponds to a synaptic complex with antiparallel alignment of recombination core sites, the other two correspond to parallel alignment of cores. We show that all three solutions can be unified into a single three-dimensional model for Xer recombination. Thus the three distinct mathematical solutions do not necessarily represent distinct three-dimensional pathways, and in this case the three distinct tangle solutions are different planar projections of the same three-dimensional configuration. Keywords: site-specific recombination; Xer recombination; topological mechanism; tangle equations; DNA knots *Corresponding author IntroductionSite-specific recombinases catalyze the exchange of genetic material between specific sites on a DNA molecule. This recombination mediates a number of biologically important processes including: integration and excision of viral DNA into and out of its host genome; inversion of DNA segments to regulate gene expression; resolution of multimeric DNA molecules to allow proper segregation at cell division; and plasmid copy number regulation. 1,2 Recombination reactions can be divided into two stages, synapsis and strand-exchange. In the first stage, the two recombination sites are brought together by the recombinase and accessory proteins to form a specific synaptic complex. In the second stage, the DNA strands are cleaved, exchanged and religated within this synapse, to form recombinant products. When the DNA substrate is circular, topological changes associated with recombination can be observed and quantified. These topological changes can be used to infer topological details of the synaptic complex and the strand-exchange mechanism, 3,4 and can be analyzed mathematically using the tangle method (reviewed in the next section). Site-specific recombinases are divided into two families, based on sequence similarity and reaction mechanism: the tyrosine recombinases, which include Flp, Cre, Int and XerC/XerD and recombine through a Holliday junction (HJ) intermediate; 6,7 and the serine recombinases, which include Tn3 and gd resolvases, as well as DNA invertases such as Gin, and recombine via double-strand cleaved intermediates. 8Many serine recombinases display topological selectivity, i.e. they distinguish between sites in different orientations, and between inter-and intramolecular sites. These systems also display topological specificity, i.e. the topology of the substrate uniquely determines the topology of the reaction product. Topological specificity implies that...

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“…-Form DNA was prepared by restriction digestion of figureeight DNA (McCulloch et al 1994) with ScaI and StyI, essentially as described (Zerbib et al 1997). Concentrations of -form DNA are expressed in moles of junctions.…”

Section: Proteins and Dnamentioning

confidence: 99%

Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of Holliday junction resolution

Gool¹,

Hajibagheri²,

Stasiak³

et al. 1999

Genes & Development

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Genetic recombination can lead to the formation of intermediates in which DNA molecules are linked by Holliday junctions. Movement of a junction along DNA, by a process known as branch migration, leads to heteroduplex formation, whereas resolution of a junction completes the recombination process. Holliday junctions can be resolved in either of two ways, yielding products in which there has, or has not, been an exchange of flanking markers. The ratio of these products is thought to be determined by the frequency with which the two isomeric forms (conformers) of the Holliday junction are cleaved. Recent studies with enzymes that process Holliday junctions in Escherichia coli, the RuvABC proteins, however, indicate that protein binding causes the junction to adopt an open square-planar configuration. Within such a structure, DNA isomerization can have little role in determining the orientation of resolution. To determine the role that junction-specific protein assembly has in determining resolution bias, a defined in vitro system was developed in which we were able to direct the assembly of the RuvABC resolvasome. We found that the bias toward resolution in one orientation or the other was determined simply by the way in which the Ruv proteins were positioned on the junction. Additionally, we provide evidence that supports current models on RuvABC action in which Holliday junction resolution occurs as the resolvasome promotes branch migration.

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Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo.

Cited by 74 publications

References 55 publications

Interaction of Branch Migration Translocases with the Holliday Junction-resolving Enzyme and Their Implications in Holliday Junction Resolution

Interaction of Branch Migration Translocases with the Holliday Junction-resolving Enzyme and Their Implications in Holliday Junction Resolution

Tangle Analysis of Xer Recombination Reveals only Three Solutions, all Consistent with a Single Three-dimensional Topological Pathway

Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of Holliday junction resolution

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