Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

HOMOLOGOUS RECOMBINATION
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sequences, that is, segments of double helix that are very similar or identical in
nucleotide sequence. This exchange allows one stretch of duplex DNA to act as
a template to restore lost or damaged information on a second stretch of duplex
DNA. Because the template for repair is not limited to the strand complementary
to that containing the damage, homologous recombination can repair many types
of DNA damage. It is, for example, the main way to accurately repair double-strand
breaks, as introduced in the previous section (see Figure 5–45B). Double-strand
breaks can result from radiation and reactive chemicals, but most of the time they
arise from DNA replication forks that become stalled or broken independently
of any such external cause. Homologous recombination accurately corrects these
accidents and, because they occur during nearly every round of DNA replication,
this repair mechanism is essential for every proliferating cell. Homologous
recombination is perhaps the most versatile DNA repair mechanism available to
the cell; the “all-purpose” nature of recombinational repair probably explains why
its mechanism and the proteins that carry it out have been conserved in virtually
all cells on Earth.
Additionally, we shall see that homologous recombination plays a special role
in sexually reproducing organisms. During meiosis, a key step in gamete (sperm
and egg) production, it catalyzes the orderly exchange of bits of genetic information
between corresponding (homologous) maternal and paternal chromosomes
to create new combinations of DNA sequences in the chromosomes passed to the
offspring.
Homologous Recombination Has Common Features in All Cells
The current view of homologous recombination as a critical DNA repair mechanism
in all cells evolved slowly from its original discovery as a key component in
the specialized process of meiosis in plants and animals. The subsequent recognition
that homologous recombination also occurs in unicellular organisms made
it much more amenable to molecular analyses. Thus, most of what we know about
the biochemistry of genetic recombination was originally derived from studies of
bacteria, especially of E. coli and its viruses, as well as from experiments with simple
eukaryotes such as yeasts. For these organisms with short generation times
and relatively small genomes, it was possible to isolate a large set of mutants with
defects in their recombination processes. The protein altered in each mutant was
then identified and, ultimately, studied biochemically. Close relatives of these
proteins have been found in more complex eukaryotes including flies, mice, and
humans, and more recently, it has been possible to directly analyze homologous
recombination in these species as well. These studies reveal that the fundamental
processes that catalyze homologous recombination are common to all cells.
DNA Base-Pairing Guides Homologous Recombination
The hallmark of homologous recombination is that it takes place only between
DNA duplexes that have extensive regions of sequence similarity (homology). Not
surprisingly, base-pairing underlies this requirement, and two DNA duplexes that
are undergoing homologous recombination “sample” each other’s DNA sequence
by engaging in extensive base-pairing between a single strand from one DNA
duplex and the complementary single strand from the other. The match need not
be perfect, but it must be very close for homologous recombination to succeed.
In its simplest form, this type of base-pairing interaction can be mimicked in
a test tube by allowing a DNA double helix to re-form from its separated single
strands. This process, called DNA renaturation or hybridization, occurs when a
rare random collision juxtaposes complementary nucleotide sequences on two
matching DNA single strands, allowing the formation of a short stretch of double
helix between them. This relatively slow helix-nucleation step is followed by a very
rapid “zippering” step, as the region of double helix is extended to maximize the
number of base-pairing interactions (Figure 5–47).