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

TRANSPOSITION AND CONSERVATIVE SITE-SPECIFIC RECOMBINATION
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When used as a repair mechanism, homologous recombination occurs between
a damaged DNA molecule and its recently duplicated sister molecule, with the
undamaged duplex acting as a template to repair the damaged copy flawlessly.
In meiosis, homologous recombination is initiated by deliberate, carefully regulated
double-strand breaks and occurs preferentially between the homologous chromosomes
rather than the newly replicated sister chromatids. The outcome can be
either two chromosomes that have crossed over (that is, chromosomes in which the
DNA on either side of the site of DNA pairing originates from two different homologs)
or two non-crossover chromosomes. In the latter case, the two chromosomes
that result are identical to the original two homologs, except for relatively minor
DNA sequence changes at the site of recombination.
TRANSPOSITION AND CONSERVATIVE SITE-SPECIFIC
RECOMBINATION
We have seen that homologous recombination can result in the exchange of DNA
sequences between chromosomes. However, the order of genes on the interacting
chromosomes typically remains the same following homologous recombination,
inasmuch as the recombining sequences must be very similar for the
process to occur. In this section, we describe two very different types of recombination—transposition
(also called transpositional recombination) and conservative
site-specific recombination—that do not require substantial regions of DNA
homology. These two types of recombination reactions can alter gene order along
a chromosome and can cause unusual types of mutations that introduce whole
blocks of DNA sequence into the genome.
Transposition and conservative site-specific recombination are largely dedicated
to moving a wide variety of specialized segments of DNA—collectively
termed mobile genetic elements—from one position in a genome to another. We
will see that mobile genetic elements can range in size from a few hundred to tens
of thousands of nucleotide pairs, and each typically carries a unique set of genes.
Often, one of these genes encodes a specialized enzyme that catalyzes the movement
of only that element, thereby making this type of recombination possible.
Virtually all cells contain mobile genetic elements (known informally as
“jumping genes”). As explained in Chapter 4, over evolutionary time scales, they
have had a profound effect on the shaping of modern genomes. For example,
nearly half of the human genome can be traced to these elements (see Figure
4–62). Over time, random mutation has altered their nucleotide sequences, and,
as a result, only a few of the many copies of these elements in our DNA are still
active and capable of movement. The remainder are molecular fossils whose existence
provides striking clues to our evolutionary history.
Mobile genetic elements are often considered to be molecular parasites (they
are also termed “selfish DNA”) that persist because cells cannot get rid of them;
they certainly have come close to overrunning our own genome. However, mobile
DNA elements can provide benefits to the cell. For example, the genes they carry
are sometimes advantageous, as in the case of antibiotic resistance in bacterial
cells, discussed below. The movement of mobile genetic elements also produces
many of the genetic variants upon which evolution depends, because, in addition
to moving themselves, mobile genetic elements occasionally rearrange neighboring
sequences of the host genome. Thus, spontaneous mutations observed in Drosophila,
humans, and other organisms are often due to the movement of mobile
genetic elements. While many of these mutations will be deleterious to the organism,
some will be advantageous and may spread throughout the population. It is
almost certain that much of the variety of life we see around us originally arose
from the movement of mobile genetic elements.
In this section, we introduce mobile genetic elements and describe the mechanisms
that enable them to move around a genome. We shall see that some of
these elements move through transposition mechanisms and others through conservative
site-specific recombination. We begin with transposition, as there are
many more known examples of this type of movement.