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8: Recombination of DNA

The chapter on mutation and repair of DNA dealt mainly with small changes in DNA sequence, usually single base pairs, resulting from errors in replication or damage to DNA. The DNA sequence of a chromosome can change in large segments as well, by the processes of recombination and transposition. Recombination is the production of new DNA molecule(s) from two parental DNA molecules or different segments of the same DNA molecule; this will be the topic of this chapter. Transposition is a highly specialized form of recombination in which a segment of DNA moves from one location to another, either on the same chromosome or a different chromosome; this will be discussed in the next chapter.

  • 8.1: Types and Examples of Recombination
    At least four types of naturally occurring recombination have been identified in living organisms: (1) General or homologous recombination, (2) Illegitimate or nonhomologous recombination, (3) Site-specific recombination, and (4) replicative recombination.
  • 8.2: Detecting Recombination
    Mendel’s Second Law described the random assortment of alleles of pairs of genes. However, certain pairs of genes show deviations from this random assortment, leading to the conclusion that those genes are linked on a chromosome. The linkage is not always complete, meaning that nonparental genotypes are seen in a proportion of the progeny. This is explained by crossing over between the gene pairs during meiosis in the parents.
  • 8.3: Meiotic Recombination
    The ability of homologous chromosomes to be paired during the first phase of meiosis is fundamental to the success of this process, which maintains a correct haploid set of chromosomes in the germ cell. Recombination is an integral part of the pairing of homologous chromosomes. It occurs between non-sister chromatids during the pachytene stage of meiosis I (the first stage of meiosis) and possibly before, when the homologous chromosomes are aligned in zygotene.
  • 8.4: Advantages of Genetic Recombination
    Not only is recombination needed for homologous pairing during meiosis, but recombination has at least two additional benefits for sexual species. It makes new combinations of alleles along chromosomes, and it restricts the effects of mutations largely to the region around a gene, not the whole chromosome. Since each chromosome undergoes at least one recombination event during meiosis, new combinations of alleles are generated.
  • 8.5: Evidence for Heteroduplexes from Recombination in Fungi
    The mechanism by which recombination occurs has been studied primarily in fungi, such as the budding yeast Saccharomyces cerevisiae and the filamentous fungus Ascomycetes, and in bacteria. The fungi undergo meiosis, and hence some aspects of their recombination systems may be more similar to that of plants and animals than is that of bacteria. However, the enzymatic functions discovered by genetic and biochemical studies of recombination in bacteria have counterparts in eukaryotic organisms too.
  • 8.6: Holliday Model for General Recombination - Single Strand Invasion
    In 1964, Robin Holliday proposed a model that accounted for heteroduplex formation and gene conversion during recombination. Although it has been supplanted by the double-strand break model (at least for recombination in yeast and higher organisms), it is a useful place to start. It illustrates the critical steps of pairing of homologous duplexes, formation of a heteroduplex, formation of the recombination joint, branch migration and resolution.
  • 8.7: Double-strand-break model for Recombination
    Several lines of evidence, primarily from studies of recombination in yeast, required changes to the reciprocal exchange of DNA chains initiated at single-strand nicks. As just mentioned, one DNA duplex tended to be the donor of information and the other the recipient, in contrast to the equal exchange predicted by the original Holliday model. Also, in yeast, recombination could be initiated by double-strand breaks.
  • 8.8: Enzymes required for recombination in E. coli
    The initial steps in finding enzymes that carry out recombination were genetic screens for mutants of E. coli that are defective in recombination. Assays were developed to test for recombination, and mutants that showed a decrease in recombination frequency were isolated. These were assigned to complementation groups called recA, recB, recC, recD, and so forth. Roughly 20 different genes (different rec complementation groups) have been identified in E. coli.
  • 8.9: Generation of Single Strands
    One of the major pathways for generating 3’ single-stranded termini uses the RecBCD enzyme, also known as exonuclease V. The three subunits of this enzyme are encoded by the genes recB, recC, and recD. Each model for recombination requires a single-strand with with a free end for strand invasion, and this enzyme does so, but with several unexpected features.
  • 8.10: Synapsis and Invasion of Single Strands
    The pairing of the two recombining DNA molecules (synapsis) and invasion of a single strand from the initiating duplex into the other duplex are both catalyzed by the multi-functional protein RecA. This invasion of the duplex DNA by a single stranded DNA results in the replacement of one of the strands of the original duplex with the invading strand, and the replaced strand is displaced from the duplex. Hence this reaction can also be called strand assimilation or strand exchange.
  • 8.11: Branch Migration
    The movement of a Holliday junction to generate additional heteroduplex requires two proteins. One is the RuvA tetramer, which recognizes the structure of the Holliday junction. The other is RuvB, which is an ATPase. It forms hexameric rings that provide the motor for branch migration.
  • 8.12: Resolution
    RuvC is the endonuclease that cleaves the Holliday junctions. It forms dimers that bind to the Holliday junction; recent data indicate an interaction among RuvA, RuvB and RuvC as a complex at the Holliday junction. The structure of the RuvA-Holliday junction complex suggests that the open structure of the junction stabilized by the binding of RuvA may expose a surface that is recognized by Ruv C for cleavage.
  • 8.E: Recombination of DNA (Exercises)

Suggested readings

  • Holliday, R. (1964) A mechanism for gene conversion in fungi. Genetics Research 5: 282-304.
  • Orr-Weaver, T. L., Szostak, J. W. and Rothstein, R. J. (1981) Yeast transformation: a model system for the study of recombination. Proc. Natl. Acad. Sci. USA 78: 6354-6358.
  • Szostak, J. W., Orr-Weaver, T. L., Rothstein, R. J. and Stahl, F. W. (1983) The double-strand-break repair model for recombination. Cell 33: 25-35.
  • Stahl, F. W. (1994) The Holliday junction on its thirtieth anniversary. Genetics 138: 241-246.
  • Kowalczykowski, S.C., Dixon, D. A., Eggleston, A. K., Lauder, S. D. and Rehrauer, W. M. (1994) Microbiological Reviews 58:401-465.
  • Eggleston, A. K. and West, S. C. (1996) Exchanging partners: recombination in E. coli. Treand in Genetics 12: 20-25.
  • Edelmann, W. and Kucherlapati, R. (1996) Role of recombination enzymes in mammalian cell survival. Proc. Natl. Acad. Sci. USA 93: 6225-6227.