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

292 Chapter 5: DNA Replication, Repair, and Recombination
Different Transposable Elements Predominate in Different
Organisms
We have described several types of transposable elements: (1) DNA-only transposons,
the movement of which is based on DNA breaking and joining reactions; (2)
retroviral-like retrotransposons, which also move via DNA breakage and joining,
but where RNA has a key role as a template to generate the DNA recombination
substrate; and (3) nonretroviral retrotransposons, in which an RNA copy of the
element is central to the incorporation of the element into the target DNA, acting
as a direct template for a DNA target-primed reverse transcription event.
Intriguingly, different types of transposons predominate in different organisms.
For example, the vast majority of bacterial transposons are DNA-only types,
with a few related to the nonretroviral retrotransposons also present. In yeasts, the
main mobile elements are retroviral-like retrotransposons. In Drosophila, DNAbased,
retroviral, and nonretroviral transposons are all found. Finally, the human
genome contains all three types of transposon, but as discussed below, their evolutionary
histories are strikingly different.
Genome Sequences Reveal the Approximate Times at Which
Transposable Elements Have Moved
The nucleotide sequence of the human genome provides a rich fossil record of
the activity of transposons over evolutionary time spans. By carefully comparing
the nucleotide sequences of the approximately 3 million transposable element
remnants in the human genome, it has been possible to broadly reconstruct the
movements of transposons in our ancestors’ genomes over the past several hundred
million years. For example, the DNA-only transposons appear to have been
very active well before the divergence of humans and Old World monkeys (25–35
million years ago), but because they gradually accumulated inactivating mutations,
they have been dormant in the human lineage since that time. Likewise,
although our genome is littered with relics of retroviral-like retrotransposons,
none appear to be active today. Only a single family of retroviral-like retrotransposons
is believed to have transposed in the human genome since the divergence
of human and chimpanzee approximately 6 million years ago. The nonretroviral
retrotransposons are also ancient, but in contrast to other types, some are still
moving in our genome, as mentioned previously. For example, it is estimated
that de novo movement of an Alu element is seen once in every 100–200 human
births. The movement of nonretroviral retrotransposons is responsible for a small
but significant fraction of new human mutations—perhaps two mutations out of
every thousand.
The situation in mice is significantly different. Although the mouse and human
genomes contain roughly the same density of the three types of transposons, both
types of retrotransposons are still actively transposing in the mouse genome,
being responsible for approximately 10% of new mutations.
Although we are only beginning to understand how the movements of transposons
have shaped the genomes of present-day mammals, it has been proposed
that bursts in transposition activity could have been responsible for critical speciation
events during the radiation of the mammalian lineages from a common
ancestor, a process that began approximately 170 million years ago. At present, we
can only wonder how many of our uniquely human qualities arose from the past
activity of the many mobile genetic elements whose remnants are found today
scattered throughout our chromosomes.
Conservative Site-Specific Recombination Can Reversibly
Rearrange DNA
A different kind of recombination mechanism, known as conservative site-specific
recombination, rearranges other types of mobile DNA elements. In this pathway,
breakage and joining occur at two special sites, one on each participating DNA