Transposons eukaryotic

RNAi probably evolved initially in primitive organisms in order to protect their genomes from viruses, transposons and additional insertable genetic elements, and to regulate gene expression. The RNAi pathway was first discovered in plants, but it is now known to function in most, if not all, eukaryotes. 

Eukaryotes also have transposons, structurally similar to bacterial transposons, and some use similar transposition mechanisms. In other cases, however, the mechanism of transposition appears to involve an RNA intermediate. Evolution of these transposons is intertwined with the evolution of certain classes of RNA viruses. Both are described in the next chapter. 

Some well-characterized eukaryotic DNA transposons from sources as diverse as yeast and fruit flies have a structure very similar to that of retroviruses these are sometimes called retrotransposons (Fig. 26-33). Retro-transposons encode an enzyme homologous to the retroviral reverse transcriptase, and their coding regions are flanked by LTR sequences. They transpose from one position to another in the cellular genome by means of an RNA intermediate, using reverse transcriptase to make a DNA copy of the RNA, followed by integration of the DNA at a new site. Most transposons in eukaryotes use this mechanism for transposition, distinguishing them from bacterial transposons, which move as DNA directly from one chromosomal location to another (see Fig. 25-43). 

FIGURE 26-33 Eukaryotic transposons. The Ty element of the yeast Saccharomyces and the copia element of the fruit fly Drosophila serve as examples of eukaryotic transposons, which often have a structure similar to retroviruses but lack the env gene. The 8 sequences of the Ty element are functionally equivalent to retroviral LTRs. In the copia element, int and RT are homologous to the integrase and reverse transcriptase segments, respectively, of the pol gene. 

Retrotransposons lack an env gene and so cannot form viral particles. They can be thought of as defective viruses, trapped in cells. Comparisons between retroviruses and eukaryotic transposons suggest that reverse transcriptase is an ancient enzyme that predates the evolution of multicellular organisms. 

Many eukaryotic transposons are related to retroviruses, and their mechanism of transposition includes an RNA intermediate. 

One of the best known eukaryotic transposons is the P element of Drosophila, which transposes only within the germ line cells of developing embryos, somatic cells being unaffected.265 625 626 It belongs to... 

For eukaryotic transposons, assembly of a transpososome is also required for transposition. The Hermes transposase is active as a hexamer on DNA (10) and Himarl transposase is active as a tetramer (11), although it remains unclear whether the Mosl transposase is active as a dimer or a tetramer (12, 13). For the well-described P Element, the transposase is active as a tetramer, and it has been reported recently that GTP acts as an allosteric cofactor for synapsis (14). 

Additional regulatory mechanisms can involve various host proteins (i.e., not encoded by the transposon) that are involved in transposome assembly and/or activity. For example, the Escherichia coli histone-like proteins IHF and HU are required for bacteriophage Mu. IHF and HNS, although not required, stimulate TnlO (IS70) transposition. A more systematic smdy has revealed several additional host factors that affect transposition of various TE in E. coli either positively or negatively (15). Finally, in the case of the eukaryotic transposon. Sleeping Beauty, the HMG protein is required for integration. 

This type of second strand management is found in eukaryotic transposable elements, such as the hAT group (28), and in V(D)J immunoglobulin-gene rearrangements (2) (Fig. Id). In these cases, however, hairpin formation occurs on the equivalent of the transposon flanks rather than on the transposon itself. In the case of V(D)J, no specific subterminal T exists, and in the case of the hAT transposons, the hairpin is formed on the transposon flank and can vary between different hAt copies. Thus, hairpin formation in these cases occurs on sequences that are not necessarily conserved, and it seems unlikely that it involves a specific flipped-out T residue. 

Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 2001 98 8714-8719. 

A FIGURE 10-8 Classification of mobile elements into two major classes, (a) Eukaryotic DNA transposons (orange) move via a DNA intermediate, which is excised from the donor site. 

Most mobile elements in bacteria transpose directly as DNA. In contrast, most mobile elements in eukaryotes are retrotransposons, but eukaryotic DNA transposons also occur. Indeed, the original mobile elements discovered by Barbara McClintock are DNA transposons. 

Eukaryotic DNA Transposons McCllntock s original discovery of mobile elements came from observation of certain spontaneous mutations in maize that affect production of any of the several enzymes required to make anthocyanln, a purple pigment in maize kernels. Mutant kernels are white, and wild-type kernels are purple. One class of these mutations is revertlble at high frequency, whereas a second class of mutations does not revert unless they occur in the presence of the first class of mutations. McClintock called the agent responsible for the first class of mutations the activator (Ac) element and those responsible for the second class dissociation (Ds) elements because they also tended to be associated with chromosome breaks. 

Since McClintock s early work on mobile elements in corn, transposons have been identified in other eukaryotes. For Instance, approximately half of all the spontaneous mutations observed in Drosophila are due to the Insertion of mobile elements. Although most of the mobile elements in Drosophila function as retrotransposons, at least one—the P element—functions as a DNA transposon, moving by a cut-and-paste mechanism similar to that used by bacterial insertion sequences. Current methods for constructing transgenic Drosophila depend on engineered, high-level expression of the P-element transposase and use of the P-element Inverted terminal repeats as targets for transposition. 

Although DNA transposons, similar in structure to bacterial IS elements, occur in eukaryotes (e.g., the Drosophila P element), retrotransposons generally are much more abundant, especially in vertebrates. 

Retroviruses of vertebrates are, perhaps, the most widely studied class of eukaryotic transposable elements. These RNA viruses use reverse transcriptase to synthesize a circular duplex DNA, which can integrate into many sites of the host cell chromosome. The integrated retroviral genome bears remarkable resemblance to a bacterial composite transposon (compare Figure 25.38 with Figure 25.35). 

Transposable elements in eukaryotic cells show striking resemblances to retroviruses in sequence organization. The term retrotransposon is used to denote this class of elements. These similarities are illustrated in Figure 25.39 for two retroviruses Ty, a transposon of yeast copia and 412, transposable elements in Drosophila, and LAP, a transposon found in the mouse genome. 

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