scholarly journals Resolution of Holliday junctions in genetic recombination: RuvC protein nicks DNA at the point of strand exchange.

1996 ◽  
Vol 93 (22) ◽  
pp. 12217-12222 ◽  
Author(s):  
R. J. Bennett ◽  
S. C. West
Keyword(s):  
Genetic Recombination ◽  
Holliday Junctions ◽  
Strand Exchange

Formation, translocation and resolution of Holliday junctions during homologous genetic recombination

1995 ◽  
Vol 347 (1319) ◽  
pp. 21-25 ◽  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Recombination ◽  
Holliday Junctions ◽  
The Novel ◽  
E Coli ◽  
The Past ◽  
Endonucleolytic Cleavage ◽  
Insight Into ◽  
Made In

Over the past three or four years, great strides have been made in our understanding of the proteins involved in recombination and the mechanisms by which recombinant molecules are formed. This review summarizes our current understanding of the process by focusing on recent studies of proteins involved in the later steps of recombination in bacteria. In particular, biochemical investigation of the in vitro properties of the E. coli RuvA, RuvB and RuvC proteins have provided our first insight into the novel molecular mechanisms by which Holliday junctions are moved along DNA and then resolved by endonucleolytic cleavage.

Genetic recombination: The nature of a crossed strand-exchange between two homologous DNA molecules

1972 ◽  
Vol 71 (3) ◽  
pp. 789-793 ◽  
Author(s):  
Nolan Sigal ◽  
Bruce Alberts
Keyword(s):  
Genetic Recombination ◽  
Strand Exchange ◽  
Dna Molecules

Structural analysis of the E. coli RUVB branch migration protein by EM and image analysis

1994 ◽  
Vol 52 ◽  
pp. 336-337
Author(s):  
X. Yu ◽  
K. Benson ◽  
A. Stasiak ◽  
I. Tsaneva ◽  
S. West ◽  
...  
Keyword(s):  
Image Analysis ◽  
Atp Hydrolysis ◽  
Genetic Recombination ◽  
Sos Response ◽  
Structure And Function ◽  
Holliday Junctions ◽  
Branch Migration ◽  
E Coli ◽  
Form Part ◽  
And Function

We have been interested in the structure and function of proteins involved in genetic recombinaton. The ruv locus on the E. coli chromosome contains three genes (ruvA, ruvB and ruvC) that are important for genetic recombination and DNA repair. The ruvA and ruvB genes form part of the SOS response to DNA damage and encode the RuvA and RuvB proteins. Together, RuvA and RuvB promote the branch migration of Holliday junctions in a reaction that requires ATP hydrolysis. Each protein plays a defined role, with RuvA responsible for DNA binding (and, in particular, junction recognition), whereas the RuvB ATPase provides the motor for branch migration. Sequence analysis has identified RuvB as a member of a superfamily of helicases, and experimentally it has been shown that RuvB, in the presence of RuvA, acts as an ATP-dependent helicase.When purified RuvB protein was incubated (in the presence of the ATP analog, ATP-γ-S) with covalently closed, relaxed dsDNA, double-ringed structures were observed on the DNA in the electron microscope (Fig. 1). The DNA must be passing through the center of these rings, since the rings are always aligned along a common axis.

scholarly journals Resolution of Mismatched Overlap Holliday Junction Intermediates by the Tyrosine Recombinase IntDOT

2017 ◽  
Vol 199 (10) ◽  
Author(s):  
Kenneth Ringwald ◽  
Sumiko Yoneji ◽  
Jeffrey Gardner
Keyword(s):  
Dna Bending ◽  
Antibiotic Resistance Genes ◽  
Product Formation ◽  
Holliday Junctions ◽  
Strand Exchange ◽  
Holliday Junction ◽  
Tyrosine Recombinase ◽  
Content Type ◽  
Tyrosine Recombinases ◽  
Overlap Region

ABSTRACT CTnDOT is an integrated conjugative element found in Bacteroides species. CTnDOT contains and transfers antibiotic resistance genes. The element integrates into and excises from the host chromosome via a Holliday junction (HJ) intermediate as part of a site-specific recombination mechanism. The CTnDOT integrase, IntDOT, is a tyrosine recombinase with core-binding, catalytic, and amino-terminal (N) domains. Unlike well-studied tyrosine recombinases, such as lambda integrase (Int), IntDOT is able to resolve Holliday junctions containing heterology (mismatched bases) between the sites of strand exchange. All known natural isolates of CTnDOT contain mismatches in the overlap region between the sites of strand exchange. Previous work showed that IntDOT was unable to resolve synthetic Holliday junctions containing mismatched bases to products in the absence of the arm-type sites and a DNA-bending protein. We constructed synthetic HJs with the arm-type sites and tested them with the Bacteroides host factor (BHFa). We found that the addition of BHFa stimulated resolution of HJ intermediates with mismatched overlap regions to products. In addition, the L1 site is required for directionality of the reaction, particularly when the HJ contains mismatches. BHFa is required for product formation when the overlap region contains mismatches, and it stimulates resolution to products when the overlap region is identical. Without this DNA bending, the N domain of IntDOT is likely unable to bind the L1 arm-type site. These findings suggest that BHFa bends DNA into the necessary conformation for the higher-order complexes, including the L1 site, that are required for product formation. IMPORTANCE CTnDOT is a mobile element that carries antibiotic resistance genes and moves by site-selective recombination and subsequent conjugation. The recombination reaction is catalyzed by an integrase IntDOT that is a member of the tyrosine recombinase family. The reaction proceeds through ordered strand exchanges that generate a Holliday junction (HJ) intermediate. Unlike other tyrosine recombinases, IntDOT can resolve HJs containing mismatched bases in the overlap region in vivo, as is the case under natural conditions. However, HJ intermediates including only IntDOT core-type sites cannot be resolved to products if the HJ intermediate contains mismatched bases. We added arm-type sites in cis and in trans to the HJ intermediates and the protein BHFa to study the requirements for higher-order nucleoprotein complexes.

scholarly journals Characterization of strand exchange activity of yeast Rad51 protein.

1997 ◽  
Vol 17 (9) ◽  
pp. 5359-5368 ◽  
Author(s):  
E Namsaraev ◽  
P Berg
Keyword(s):  
Genetic Recombination ◽  
Strand Exchange ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Ssdna Binding ◽  
Double Stranded Dna ◽  
Ssdna Binding Protein ◽  
Linear Dsdna ◽  
Circular Ssdna

The Saccharomyces cerevisiae RAD51 gene product takes part in genetic recombination and repair of DNA double strand breaks. Rad51, like Escherichia coli RecA, catalyzes strand exchange between homologous circular single-stranded DNA (ssDNA) and linear double-stranded DNA (dsDNA) in the presence of ATP and ssDNA-binding protein. The formation of joint molecules between circular ssDNA and linear dsDNA is initiated at either the 5' or the 3' overhanging end of the complementary strand; joint molecules are formed only if the length of the overhanging end is more than 1 nucleotide. Linear dsDNAs with recessed complementary or blunt ends are not utilized. The polarity of strand exchange depends upon which end is used to initiate the formation of joint molecules. Joint molecules formed via the 5' end are processed by branch migration in the 3'-to-5' direction with respect to ssDNA, and joint molecules formed with a 3' end are processed in the opposite direction.

Mismatch repair and the fidelity of genetic recombination

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 68-73 ◽  
Author(s):  
Miroslav Radman
Keyword(s):  
Homologous Recombination ◽  
Mismatch Repair ◽  
High Frequency ◽  
Genetic Recombination ◽  
Strand Exchange ◽  
High Fidelity ◽  
Rare Occurrence ◽  
Heteroduplex Dna ◽  
Noncoding Sequences ◽  
Multiple Exchange

Two modes of mismatch repair are known to operate in bacteria: long-patch mismatch repair and very short patch mismatch repair. Very short patch mismatch repair systems act on a specific mismatch by conserving only one base pair. Therefore, when very short patch mismatch repair acts on heteroduplex recombination intermediates, it hyper-recombines specific markers by creating patchwork sequences, i.e., apparent multiple exchange events, on the repaired strand. Long-patch mismatch repair is antirecombinagenic, apparently by decomposing heteroduplex DNA or aborting its formation whenever well-recognized mismatches are formed by strand exchange between nonidentical parental sequences. It is postulated here that mismatch-stimulated antirecombination by long-patch mismatch repair is a "proofreading" system assuring high fidelity of homologous recombination. This accounts for chromosomal stability in eucaryotes (i.e., the rare occurrence of chromosomal aberrations and mitotic recombination versus the high frequency of precise sister chromatid exchange), suggests a role for diverged repetitive and other noncoding sequences as chromosomal antirecombination elements, and provides a molecular mechanism for speciation without the necessity of geographical separation.Key words: mismatch repair, genetic recombination, antirecombination, elements, speciation.

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