Holliday junction processing

Re combinational DNA repair of a circular bacterial chromosome, while essential, sometimes generates deleterious byproducts. The resolution of a Holliday junction at a replication fork by a nuclease such as RuvC, followed by completion of replication, can give rise to one of two products the usual two monomeric chromosomes or a contiguous dimeric chromosome (Fig. 25-41). In the latter case, the covalently linked chromosomes cannot be segregated to daughter cells at cell division and the dividing cells become stuck. A specialized site-specific recombination system in E. coli, the XerCD system, converts the dimeric chromosomes to monomeric chromosomes so that cell division can proceed. The reaction is a site-specific deletion reaction (Fig. 25-39b). This is another example of the close coordination between DNA recombination processes and other aspects of DNA metabolism. 

An important characteristic of Holliday junctions formed from homologous duplexes is that they can move by a process called branch migration.295 Because of the twofold symmetry of the branched structure the hydrogen bonds of one base pair can be broken while those of a new base pair are formed, the branch moving as shown in Fig. 5-28. Notice that, in this example, the nonhomo-logous (boxed) base pairs TA and GC have become mispaired as TG and AC after branch migration. More significantly, the junction may be cut by a resolvase at the points marked... 

RuvC is an endonuclease that is highly specific for Holliday junctions. It is a resolvase that cuts at either points a,a or b,b of Eq. 27-11 to form either "patched" or "spliced" recombinant DNA (Fig. 27-26C). Similar resolvases process bacteriophage DNA562-564 and have also been found in yeasts and in mammals.565 566 All are dimeric metal ion-dependent proteins.567... 

In recombination pathways for meiosis and some other processes, intermediates form that are composed ot four polynucleotide chains in a crosslike structure. Intermediates with these crosslike structures are often referred to as Holliday junctions, after Robin Holliday, who proposed their role in recombination in 1964. Such intermediates have been characterized by a wide range of techniques including x-ray crystallography. 

Cre catalyzes the formation of Holliday junctions as well as their resolution. In contrast, other proteins bind to Holliday junctions that have already been formed by other processes and resolve them into separate duplexes. In many cases, these proteins also promote the process of branch migration whereby a Holliday junction is moved along the two component double helices. Branch migration can affect which segments of DNA are exchanged in a recombination process. 

Recombination is the exchange of segments between two DNA molecules. Recombination is important in some types of DNA repair as well as other processes such as meiosis, the generation of antibody diversity, and the life cycles of some viruses. Some recombination pathways are initialed by strand invasion, in which a single strand at the end of a DNA double helix forms base pairs with one strand of DNA in another double helix and displaces the other strand. A common intermediate formed in other recombination pathways is the Holliday junction, which consists of four strands of DNA that come together to form a crosslike structure. Recoinbinases promote recombination reactions through the introduction of specific DNA breaks and the formation and resolution of junction intermediates. 

Homologous recombination in E. coli is a two-step process that requires the RecA protein. In step 1, a single-stranded DNA invades the target DNA molecule and base pairs with its homologous sequence. In step 2, the heteroduplex formed in step 1 is isomerized to form a Holliday junction which is resolved by subsequent DNA cleavage and ligation reactions. 

Shinagawa H., Iwasaki H. (1996) Processing the Holliday junction in homologous recombination. Trends Biochem. Sci. 21 107. 

The Holliday junction "resolves" itself into two unbroken duplexes, by a process of strand breaking and rejoining. The process leading to recombination begins with isomerization of the Holliday structure (step 5), followed by strand breakage ... 

Processing the Holliday junction. Completion of the recombination process requires "resolution" of the Holliday intermediate by endonuclease action followed by ligation and perhaps by gap repair. The major recombination pathway in E. coli employs a binding protein, a nuclease, and a helicase encoded by genes RuvA, B, and RuvA is a DNA binding... 

Fig. 5. Two alternative models for error-free PRR via recombinational processes. (A) A strand exchange model, and (B) a template switching model. Both models propose that progression of leading strand synthesis in the presence of replicationblocking DNA damage (represented by a triangle) requires the association of the two nascent DNA strands, followed by resolution of the intermediary structure via (A) cleavage of the Holliday junction or (B) reverse branch migration. Adapted from Broomfield et al. (2001).

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