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 1; 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 previously recognized.

References :

• Bao W & Jurka J (2013) Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. Mob DNA 4: 12.
• Bikard D & Marraffini LA (2013) Control of Gene Expression by CRISPR-Cas systems. F1000Prime Rep 5: 47.
• Demerec M, Adelberg EA, Clark AJ & Hartman PE (1966) A PROPOSAL FOR A UNIFORM NOMENCLATURE IN BACTERIAL GENETICS. Genetics 54: 61-76.
• Dumesic PA & Madhani HD (2014) Recognizing the enemy within: licensing RNA-guided genome defense. Trends in Biochemical Sciences 39: 25-34.
• Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R & Davies DR (1994) Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases [see comments]. Science 266: 1981-1986.
• Fedoroff NV (2012) Transposable Elements, Epigenetics, and Genome Evolution. Science 338: 758-767.
• Hickman AB & Dyda F (2015) Mechanisms of DNA Transposition. Microbiol Spectr 3: MDNA3-0034-2014.
• Hickman AB, Chandler M & Dyda F (2010) Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Critical Reviews in Biochemistry and Molecular Biology 45: 50-69.
• Nagy Z & Chandler M (2004) Regulation of transposition in bacteria. Res Microbiol 155: 387-398.