Relationship between IS and eukaryotic TE
In spite of their obvious
similarities, there is often poor transfer of knowledge between studies of
prokaryotic and of eukaryotic TE. This artificial barrier is reflected in their
nomenclature systems: Prokaryotic TE are named following the basic logic of
bacterial genetics built on the initial Demerec rules (Demerec, et al., 1966);
Eukaryotic TE, on the other hand, have more colorful names in keeping with the
culture of nomenclature used in eukaryotic genetics. To a certain extent, this
camouflages the diversity and relationships between members of the eukaryotic
TE superfamilies and their prokaryotic cousins.
It is important to appreciate
that the basic chemistry of transposition is identical for both prokaryotic and
eukaryotic elements (Dyda, et al., 1994, Hickman, et
al., 2010, Hickman & Dyda, 2015). Moreover, many eukaryotic DNA
transposons have similar sizes and organization to those of prokaryotic IS and,
since most do not carry additional "passenger" genes, they are not transposons
in the prokaryotic sense and should strictly be considered as eukaryotic IS.
The major differences lie in how Tpase expression and activity is regulated (Nagy & Chandler, 2004). One important
difference is that most eukaryotic transposons are "insulated" by constraints
of the nucleus (which physically separate the transposition process from that
of Tpase expression) while those of prokaryotes are not since prokaryotic
transcription and translation are coupled. In addition, eukaryotic transposons
are subject to a hierarchy of regulation via small RNAs (Fedoroff, 2012, Dumesic & Madhani, 2014). In prokaryotes, it
is possible that CRISPRs may impose some control at this level but, although it
has been demonstrated that CRISPRs are active against mobile genetic elements
and may regulate some endogenous gene expression [see (Bikard & Marraffini, 2013)], these are limited to plasmids and
phage and to our knowledge have not yet been demonstrated to act on
intracellular MGE such as IS and transposons.
In spite of these differences, a
significant number of eukaryotic DNA TE are related to prokaryotic IS (Table
2), and moreover,
eukaryotic TE including passenger genes are now being identified [see e.g. (Bao & Jurka, 2013)]. This reinforces the
view that the borders between different types of TE are "fuzzier" than
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