long terminal repeat (LTR) is the control center for gene expression.
As may be expected because of the integrated phase of their
life cycle, retroviruses have somewhat typical eucaryotic promoters
with transcriptional enhancers and some also have regulatory
elements responsive to either viral or specialized cellular
(e.g. hormonal) trans-activating factors (HIV, MMTV). Enhancer
functions have also been mapped to the gag (ALSV) and gag-pol
(SIV and HIV) regions of some viruses but their role in the
virus life cycle has yet to be established. In any case, all
of the requisite signals for gene expression are found in the
LTRs: Enhancer, promoter, transcription initiation (capping),
transcription terminator and polyadenylation signal. Expression
directed by the viral LTR signals is carried out entirely by
host cell enzymes (RNA pol II, poly A synthetase, guanyl transferase).
The enhancer and other transcription regulatory signals are
contained in the U3 region of the 5' LTR, and the TATA box is
located roughly 25 bp from the beginning of the R sequence.
The presence and position of specific sequence signals used
for transcription and binding sites for known or suspected transcription
sites are shown in the figure below. The poly A addition signal
(AAUAAA) in HTLV-1 is an unusually long distance upstream from
the polyadenylation site (250 nt, by definition the end of R).
It is hypothesized that the signal is brought in proximity to
the addition site by secondary structure in the RNA.
The integrated provirus has two LTRs, and the 5' LTR normally
acts as an RNA pol II promoter. 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. Transcription
is not terminated in the 5' LTR, probably due to failure of
formation of secondary structure in the RNA which uncouples
RNA polymerase, analogous to bacterial attenuation. Occasionally
the stop signal in the 3' LTR is "read-through" and terminated
in host flanking sequences, these hybrid transcripts could then
be efficiently packaged and transmitted in virions. This process
may play an important role in transduction of oncogenes.
3' LTR is not normally functional as a promoter, although it
has exactly the same sequence arrangement as the 5' LTR. Instead,
the 3' LTR acts in transcription termination and polyadenylation.
Transcriptional interference occurs when the two LTRs are oriented
as in a provirus; the 5' LTR has dominant control as a promoter.
When the integrity of the 5' LTR is disrupted, the 3' LTR can
act as a promoter, and this is the basis for one form of retroviral
oncogenesis. Thus transcription from the 5' LTR interferes with
the function of the 3' LTR as a promoter-enhancer. Experiments
by Cullen et al. (Nature 307:239, 1984) demonstrated this phenomenon
very clearly. By progressively removing portions of a provirus
and using an indicator gene downstream of the 3' LTR, the transcriptional
activity from both LTRs could be assessed. Cellular restriction
of LTR function can occur. Transcriptional enhancers are tissue
and cell specific in their function. For retroviruses like MuLV,
embryonal tissues and cells do not host viral gene expression
whereas differentiated or adult tissues and cells express viral
RNA to high levels. These differences, which are due to enhancer
"activators" and "repressors" have been studied in cell lines
that can be differentiated in cell cultures. Changes in the
structures of the binding sites in the LTRs can be correlated
with tissue-specific expression patterns of mutant MLV and their
induction of tumor formation in those tissues.