The transposable elements that transpose via an RNA intermediate are of two kinds: Retrotransposons and retroposons.
1) Retrotransposons: They resemble retroviruses and encode reverse transcriptase enzyme.
2) Retroposons: Neither do they resemble retroviruses nor do they code for their own reverse transcriptase.
Retrotransposons: The genetic information of retroviruses is encoded in RNA, which is transcribed into DNA by the action of reverse transcriptase after the virus infects a cell. The reverse transcribed viral DNA is then inserted into the genome of the host cell, where it utilizes host cell’s machinery to express its genes. HIV is an example of a retrovirus.
Retrotransposons are similar to retroviruses in many aspects. Both have a similar structural organization, and nucleotide sequences of the two are similar. This immediately suggests that retrotransposons originated as retroviruses. Some retrotransposons even encode structural proteins that form virus-like particles in the cells. However, the most important difference between retrotransposons and retroviruses is the inability of retrotransposons to leave cells as virus particle and infect other cells. Retrotransposons have lost the ability to infect other cells; they are maintained as part of the chromosomes in cells.
Yeast Ty elements and D. melanogaster copia elements are the two prominent examples of retrotransposons. Retrotransposons are bordered by long terminal repeats (LTRs). The repeats are longer than inverted terminal repeats of transposons. Retrotransposons carry gag and pol genes that are similar to same genes found in retroviruses. During the movement of a retrotransposon in the genome, first RNA polymerase II transcribes the retrotransposon DNA into an RNA, which is polyadenylated to become mRNA. The gag and pol mRNAs are translated into polyproteins, which are cleaved into several individual proteins. The gag polyprotein is cleaved into three proteins, which form a capsid-like structure surrounding the retrotransposon RNA. The pol polyprotein is cleaved into four enzymes: reverse transcriptase, RNase, protease and integrase. Protease cleaves the polyproteins into their individual proteins; the proteins and RNA assemble into a retrovirus-like particle. Reverse transcriptase forms a single- stranded DNA molecule from the retrotransposon RNA template; RNase removes the RNA. The DNA is circularized and complementary DNA strand is synthesized to create a double-stranded, circular copy of the retrotransposon. Integrase integrates this new retrotransposon copy into a new site on the cellular DNA.