Long terminal repeat
Long terminal repeats (LTRs) are identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA. They are used by viruses to insert their genetic material into the host genomes.
The HIV-1 LTR is approximately 640 bp in length and, like other retroviral LTRs, is segmented into the U3, R, and U5 regions. U3 and U5 has been further subdivided according to transcription factor sites and their impact on LTR activity and viral gene expression. The multi-step process of reverse transcription results in the placement of two identical LTRs, each consisting of a U3, R, and U5 region, at either end of the proviral DNA. The ends of the LTRs subsequently participate in integration of the provirus into the host genome. Once the provirus has been integrated, the LTR on the 5′ end serves as the promoter for the entire retroviral genome, while the LTR at the 3′ end provides for nascent viral RNA polyadenylation and, in HIV-1, HIV-2, and SIV, encodes the accessory protein, Nef.
All of the required signals for gene expression are found in the LTRs: Enhancer, promoter (can have both transcriptional enhancers or regulatory elements), transcription initiation (such as capping), transcription terminator and polyadenylation signal.
In HIV-1, the U5 region has been characterized according to functional and structural differences into several sub-regions as follows:
- TAR or trans-acting responsive element, plays a critical role in transcriptional activation via its interaction with viral proteins. It forms a highly stable stem-loop structure consisting of 26 base pairs with a bulge secondary structure that interfaces with the viral transcription activator protein Tat.
- Poly A play roles both in dimerization and genome packaging since it is necessary for cleavage and polyadenilation. It has been reported that sequences upstream (U3 region) and downstream (U5 region) are needed in order to make the cleavage process efficient.
- PBS or primer binding site, of 18 nucleotides long, it has a specific sequence that bind to tRNALys and are requirements for initiation of reverse transcription.
- Psi (Ψ) or the packaging signal is a unique motif that is associated with this process, although is not sufficient to specify for packaging. It is composed of four stem-loop (SL) structures with a major splicing donor site embedded in the second SL.
- DIS or dimer initiation site that mediates RNA-RNA interactions. Is a highly conserved stem-loop sequence found in many retroviruses and is characterized by a conserved stem and palindromic loop, when homodimerized, forms a “kissing-loop” complex.
The transcript begins, by definition, at the beginning of R, is capped, and proceeds through U5 and the rest of the provirus, usually terminating by the addition of a poly A tract just after the R sequence in the 3' LTR.
The finding that both HIV LTRs can function as transcriptional promoters is not surprising since both elements are apparently identical in nucleotide sequence. Instead, the 3' LTR acts in transcription termination and polyadenylation. However, it has been suggested that the transcriptional activity of the 5' LTR is far greater than that of the 3' LTR, a situation that is very similar to that of other retroviruses.
During transcription of the human immunodeficiency virus type 1 provirus, polyadenylation signals present in the 5' long terminal repeat (LTR) are disregarded while the identical polyadenylation signals present in the 3'LTR are utilized efficiently. It has been suggested that transcribed sequences present within the HIV-1 LTR U3 region act in cis to enhance polyadenylation within the 3' LTR.
The LTRs are partially transcribed into an RNA intermediate, followed by reverse transcription into complementary DNA (cDNA) and ultimately dsDNA (double-stranded DNA) with full LTRs. The LTRs then mediate integration of the retroviral DNA via an LTR specific integrase into another region of the host chromosome. The first LTR sequences were derived by A.P. Czernilofsky and J. Shine in 1977 and 1980.
Retroviruses such as Human Immunodeficiency Virus (HIV) use this basic mechanism.
As 5' and 3' LTRs are identical upon insertion, the difference between paired LTRs can be used to estimate the age of ancient retroviral insertions. This method of dating is used by paleovirologists, though it fails to take into account confounding factors such as gene-conversion and homologous recombination.
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