Anthology of Human Repetitive DNA
275
Gag
is
a
multifunctional
structural
polyprotein separated into matrix, capsid,
and nucleocapsid structural proteins by
the
pro
-encoded protease (PR), which is
related to cellular aspartic proteases.
The
pol
gene encodes a polyprotein
precursor processed by the protease to
reverse transcriptase and integrase. RT
contains a ribonuclease H domain (RH),
which digests RNA strands in RNA–DNA
duplexes. RT encoded by LTR retrotrans-
posons is capable of both RNA- and
DNA-dependent DNA syntheses. It is the
most conserved endoretroviral protein.
The retroviral IN may be distantly related
to DD
35
E transposases (see Sect. 3.3.2).
The
env
-encoded protein precursor is
cleaved by the protease into the enve-
lope, surface and transmembrane glyco-
proteins. It is thought that viral particles
bind host cells through interactions be-
tween the surface glycoproteins and spe-
ciFc cell surface receptors (±ig. 8). Such
interactions trigger fusion of the cell and
virus membranes, followed by intrusion of
the virus into the cell cytoplasm.
Transcription
Transcription of the pro-
virus starts at the pol II promoter present in
the long terminal repeat (see LTR; ±ig. 8a;
±ig. 9). LTR is composed of three regions,
called U3, R, and U5. The U3 region
contains the pol II promoter. Additional
signals affecting transcription, including
enhancers, were also detected in the U3
region. The start of the LTR transcrip-
tion corresponds to the U3-R boundary.
Conversely, the R-U5 boundary is de-
Fned by the transcription stop-site. The
transcription termination is mediated by
the AATAAA or ATTAAA polyadenyla-
tion signals usually present in the U3
region. Therefore, the transcription is
terminated in the second LTR only. In
some retroviruses, including HIV, the
polyadenylation signal is placed down-
stream of the U3-R boundary. However,
the Frst LTR is still bypassed during tran-
scription, presumably due to suppression
of the transcription termination by a small
distance between the transcription start-
site and the polyadenylation signal.
Reverse transcription
Reverse transcrip-
tion of retroviral RNAs occurs in the cyto-
plasm of the infected host cell. It begins
either when the viral particles enter the cy-
toplasm or when nuclear transcription of
the already integrated provirus produces
its functional RNA. The cytoplasmic local-
ization of the retroviral reverse transcrip-
tion is in sharp contrast to nucleus-based
reverse transcription of non-LTR retro-
transposons (±ig. 4). The retroviral reverse
transcription is believed to follow a mul-
tistep process outlined schematically in
±ig. 9 and described below.
1. The reverse transcription starts with the
minus-strand DNA synthesis primed by
the 3
0
end of a tRNA molecule annealed
to the primer binding site (PBS).
Usually, the PBS is complementary to
the
18-bp 3
0
end of the virus-speciFc
tRNA that starts just a few nucleotides
downstream of the U5 region.
2. Minus-strand DNA synthesis proceeds
to the 5
0
end of the RNA, producing
a 100 to 150 bp DNA molecule called
minus-strand strong-stop DNA
,wh
ichis
released from the original RNA–DNA
duplex by the RNaseH mediated diges-
tion of the complementary RNA.
3. ±ollowing the digestion, the minus-
strand strong-stop DNA performs the
Frst strand transfer, annealing to the
R-region at the 3
0
end of the plus-
strand RNA.
4. After the strand transfer, minus-strand
DNA synthesis continues, and it is
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