Retrotransposons are a large group of transposable elements that includes retroviruses and other elements that resemble retroviruses, but have no extracellular phase (1). Well-studied retroviruses include human immunodeficiency virus (HIV) and Moloney murine leukemia virus (MoMuV). Well-studied retroviral-like elements include the Ty elements of yeast and the gypsy and copia elements of Drosophila.
The transposition substrate for retrotransposons is a DNA copy of the element generated by reverse transcription of an RNA copy of the "proviral" form of the element integrated into the genomic DNA. At the ends of this DNA copy are the special sequences, again arranged as inverted terminal repeats, that will be acted upon by the integrase. The chemical steps of transposition—that is, the DNA breakage and joining reactions that process this reverse transcription product and insert it into target DNA—are fundamentally identical to the reactions that mediate the translocation of other DNA-only transposable elements in bacteria, Drosophila, and Caenorhabditis elegans (2). Moreover, the retrotransposon integrases are related in structure to the transposases of DNA-only elements, including those from bacteria. Indeed, the active site of the bacterial transposase MuA (3), is virtually superimposable with the catalytic region of the HIV integrase (4), although there is little primary structure homology between these proteins.
A retroviral provirus found in genomic DNA has at its ends two directly repeated segments several hundred base pairs long called long terminal repeats (LTRS); at the termini of these segments are short sequences that are recognized by the integrase and mark the sites of recombination (Fig. 1). (Only the sequences at the outside tips of the LTRs are recognized as recombination sequences; recombination does not occur at the two internal sites.) The interior of the element encodes several polyproteins (gag, pol, and env) that are cleaved by element-encoded proteinases to yield their several final products. Gag includes MA, a matrix-associated protein, CA, the major structural component of the viral capsid, and NC, a nucleocapsid component that interacts with the viral genome. Pol includes reverse transcriptase, ribonuclease H, and integrase; the order of these domains does vary among different elements. Env includes several capsid proteins involved in receptor recognition and viral entry. Retrotransposons have a structure similar to retroviruses, but lack an extracellular phase. Indeed, many retrotransposons lack or contain a defective version of env, which is key for the extracellular phase.
Figure 1. Retroviruses and retrotransposons. Retroviruses and retrotransposon generate a mobile DNA copy of the element by using an element-encoded reverse transcriptase and ribonuclease H to convert an RNA copy of the element into a double-stranded DNA copy. Exposed 3′OH ends on this DNA segment, resulting either from reverse transcription or from processing by the element-encoded integrase, attack the target DNA at staggered positions (see Fig. 2 in Transposable Elements). These elements encode multiple polyproteins, gag, pol, and env: gag includes capsid components, pol includes reverse transcriptase, ribonuclease H, and integrase, and env includes functions for entry into new cells. In some, retrotransposons, the Ty1-copia class (Ty1 being a yeast element and copia a Drosophila element), no env gene is recognizable. In the Ty3-gypsy class (Ty3 being a yeast element and gypsy a Drosophila element), a defective version of env can sometimes be observed. These elements and other retrotransposons are very widespread.
Transposition begins by the transcription of the provirus by the host RNA polymerase to yield a viral RNA copy; some of these molecules serve as messenger RNA for synthesis of the viral proteins. Two copies of the RNA are packaged into the virion, which includes reverse transcriptase and integrase. Viruses bud from the cell and then bind to and enter another cell; retrotransposons move only intracellularly. While in the virion, the RNA is converted to double-stranded DNA. This resulting DNA, with assembled viral proteins, enters into the nucleus, where integration occurs. As with other transposons, insertions of these elements can disrupt genes or bring host genes under the control of viral enhancers.
The substrate for transposition is the DNA copy of the element. Recombination often initiates with the cleavage by integrase of several nucleotides from the 3′ ends of the DNA, to expose the actual element termini, although in some elements this trimming step is not necessary. Thus, as with DNA-only elements, exposing the 3′OH ends of the transposon is a key step. The integrase then promotes the attack of these 3′OH ends on staggered positions in the target DNA; because of this stagger, the newly inserted transposon is flanked by short gaps that will be repaired by the host DNA repair machinery, resulting in target site duplications of a characteristic length for each element.
