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Yapeng Gu and Wesley I. Sundquist
A powerful arm of the cellular defence against microbial invaders has
been characterized. APOBEC3G, a protein that can fight off HIV, works by
introducing ‘typographical errors’ during viral replication.
IV encodes a protein that allows the
virus to multiply in otherwise resistant human cells1–3. This protein, Vif
— for ‘viral infectivity factor’ — works by
overcoming a cellular protein, APOBEC3G,
whose task is to inhibit the replication
of HIV and other retroviruses4. As they
describe in Cell 5 and on pages 94 and 99 of
this issue6,7, three groups have now discovered how APOBEC3G hampers viral replication. The authors find that, as the
retroviral RNA genome is copied into DNA
in host cells, this protein changes ‘C’s to ‘U’s
in the DNA. APOBEC3G therefore represents a remarkable innate cellular defence
mechanism that drastically alters the chemical composition and coding capacity of
replicating retroviruses.
Retroviruses, which include HIV and
murine leukaemia virus (MLV), have
genomes that are made up of single-stranded
RNA. For these viruses to replicate in a host
cell, a double-stranded DNA copy of the
RNA genome must be made, by the process
of reverse transcription. This happens in two
steps. First, a DNA strand that has a sequence
complementary to the RNA is produced
(this is called ‘minus-strand’DNA).Then the
RNA is removed and a second (plus-strand)
DNA molecule, complementary to the first
(and therefore matching the sequence of the
H
original RNA), is synthesized. The resulting
double-stranded DNA is incorporated into
the host-cell genome, and, when switched
on, is used to generate the proteins and RNA
needed to form new virus particles (virions).
It has been known for more than a decade
that the Vif protein is required for HIV to
replicate in some human cell types (termed
‘non-permissive’ cells), but not others
(‘permissive’ cells)1–3. Non-permissive cells
express APOBEC3G (also known as CEM15),
and permissive cells become non-permissive
upon expression of this protein4. These and
other data indicate that APOBEC3G blocks
viral replication, and that Vif works by overcoming this block. However, the precise
nature of the replication block has not been
clear — and it is unusual in that it is manifest
after the virus has entered a new target cell.So,
Vif-deficient viruses produced by non-permissive cells are released at normal levels, but
are somehow impaired in their ability to form
stable, productive replication intermediates
when they enter new target cells3,8.
Clues to how this might happen have
come from several observations. First,
APOBEC3G can be packaged into HIV-1
virions4. Second, APOBEC3G is related to a
family of enzymes that catalyse the deamination of cytosine bases (C’s) in DNA and
RNA, thereby producing uracils (U’s).
Finally, APOBEC3G can mutate the DNA of
the bacterium Escherichia coli 9. Thus it was
suggested that APOBEC3G might inhibit
HIV replication by altering the coding capacity of viral RNA or DNA4.
Harris et al.5, Mangeat et al.6 and Zhang
et al.7 have now shown that APOBEC3G
can indeed alter the sequences of the HIV
and other retroviral genomes, producing an
exceptionally high frequency of guanineto-adenosine (G-to-A) substitutions in the
plus (protein-coding) strand of the viral
DNA.As shown in detail in Fig. 1, this observation implies that APOBEC3G changes C’s
to U’s in the DNA minus strand during
replication (because, when the plus strand is
made using the minus strand as a template,
G’s are inserted opposite C’s, but A’s opposite U’s). Importantly, G-to-A hypermutation is suppressed by the presence of
Vif 5–7,10, and APOBEC3G has the required
deaminase activity5,7 and can act on singlestranded DNA substrates5. Deamination
by APOBEC3G is quite promiscuous, but
exhibits some sequence selectivity, with a
preference for C/T–C–C sequences5–7.
Conversion of C’s to U’s in the genomic
DNA minus strand apparently blocks viral
replication in several ways (Fig. 1). First, the
presence of uracils can target the minus
strand for destruction.Uracil is not normally
found in DNA and can therefore be excised
by host DNA-repair enzymes. This could
Target cell
APOBEC3G
Vif
?
3′
G
G
G
Genomic V
RNA
tRNA
5′
(–)
5′
Strand breakage
APOBEC3G
U
(+)(–)
primers
Reverse G C
Reverse
transcription
transcription
Second- 3′5′
U synthesis
GC
Infection
5′
Deamination
O
N
O
O P O
HN
N
O
O
O
O
O P O
O
H
H
AU
NH2
3′
O
Destruction
Plus-strand DNA
synthesis impaired
U strand
GC
Viral RNA
Uracil-DNA glycosylase
Minus-strand DNA (–)
Vif
RNA
?
H
H
Figure 1 Editing HIV: how the cellular APOBEC3G protein might inhibit
HIV replication5–7,10. From left, APOBEC3G has been packaged, together
with the viral genome, in a viral particle. Then, when the retrovirus enters
a new cell, the viral reverse transcriptase copies the genomic RNA into a
double-stranded DNA. Replication begins at a tRNA primer (purple), and
creates first a DNA minus (1) strand that is a complementary copy of the
RNA, and then a DNA plus (+) strand that is a complementary copy of the
minus strand. However, APOBEC3G deaminates 28-deoxycytidines (C) in
H
H
2′-deoxycytidine
AU
N
O
O
H
3′
O
H
H
G-to-A hypermutation
AU
H
5′
3′
Plus-strand
editing and repair?
2′-deoxyuridine
the minus strand, producing 28-deoxyuridines (U). Plus-strand synthesis
then converts these C-to-U changes into G-to-A mutations, because C pairs
with G, whereas U pairs with A. C-to-U conversion can diminish HIV-1
replication in several ways: deglycosylation of uracil can lead to strand
breakage and destruction; the presence of U’s can reduce plus-strand
synthesis11; and G-to-A hypermutations in the viral genome can impair all
subsequent viral functions. The viral Vif protein blocks the effects of
APOBEC3G through an as yet undefined mechanism.
NATURE | VOL 424 | 3 JULY 2003 | www.nature.com/nature
21
© 2003 Nature Publishing Group
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eventually lead to strand breakage and
destruction — explaining the apparent
instability of viral reverse transcripts. Second, uracils in the minus strand can impair
the initiation of plus-strand synthesis during
HIV-1 reverse transcription11. Finally, even
when complete, double-stranded DNA
copies of the viral genome are made, they
contain many G-to-A mutations, which
result in amino-acid changes and aberrant
‘stop’ signals in the encoded proteins, and
generally reduce viral fitness at every subsequent stage in replication6. The biased Gto-A mutation profile might also explain the
overall A-richness of the HIV-1 genome, as
well as the non-lethal hypermutation sometimes observed during viral replication5–7,10.
As with all other immune responses,
APOBEC3G must successfully distinguish
between ‘self ’ and ‘non-self ’. So it is remarkable that, as two of the groups show, the protein can inhibit the infectivity of retroviruses
that differ markedly in sequence, including
MLV5,6, simian immunodeficiency virus,
equine infectious anaemia virus (EIAV), and
even engineered retroviruses — derived from
HIV-1 — that contain little of the original
genome6. Presumably, these genomes are
specifically targeted because APOBEC3G is
incorporated into virus particles, and/or
because only virus-specific intermediates are
selected for deamination. It will therefore
be important to learn how APOBEC3G is
packaged into virions, and how it selects its
substrates. Intriguingly, another member of
this enzyme family, AID (activation-induced
cytidine deaminase), which is involved in
antibody-gene diversification, also targets
single-stranded DNA. It requires transcription of the targeted gene into RNA12,13, and
the presence of an RNA-degrading enzyme13.
By analogy, APOBEC3G might target singlestranded minus DNA after reverse transcription and removal of the RNA template by
the RNA-degrading activity of the reverse
transcriptase enzyme. Alternatively, substrate
targeting could be mediated by a cofactor, as
is the case for another family member14.
Another issue, which could have therapeutic implications, is how Vif overcomes
the antiviral activity of APOBEC3G. Possibilities include downregulation of APOBEC3G
protein levels, exclusion of the protein from
progeny virions, and inactivation of incorporated APOBEC3G molecules4. Moreover,
do viruses such as MLV and EIAV, which
do not have the Vif gene, avoid the effects
of APOBEC3G by expressing other proteins with Vif-like activities? Or do they
simply replicate only in host cells that lack
APOBEC3G?
It is becoming increasingly apparent that
cells have evolved a remarkable number of
mechanisms to defend themselves from
microbial invaders, and that microbes have
discovered clever ways to circumvent those
defences. Retroviruses are particularly good
tools with which to study innate cellular
immune systems, because the battle between
cells and retroviruses is an ancient and
intense one — as exemplified by the fact that
retroviral elements make up an astonishing
8% of the human genome15. Other cellular
defences against retroviruses include ZAP, a
protein that targets viral messenger RNAs for
destruction16, and Fv-1 (and related cellular
proteins), which inhibits early stages of
retroviral replication17,18. The molecular
description of APOBEC3G activity 5–7,10 has
revealed yet another arm of the innate
immune system, in which cells actually edit
the genomes of invading retroviruses.
■
Yapeng Gu and Wesley I. Sundquist are in the
Department of Biochemistry, University of Utah,
Salt Lake City, Utah 84132, USA.
e-mail: [email protected]
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4. Sheehy, A. M., Gaddis, N. C., Choi, J. D. & Malim, M. H. Nature
418, 646–650 (2002).
5. Harris, R. S. et al. Cell 113, 803–809 (2003).
6. Mangeat, B. et al. Nature 424, 99–102 (2003).
7. Zhang, H. et al. Nature 424, 94–98 (2003).
8. von Schwedler, U., Song, J., Aiken, C. & Trono, D. J. Virol. 67,
4945–4955 (1993).
9. Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. Mol. Cell
10, 1247–1253 (2002).
10. Lecossier, D., Bouchonnet, F., Clavel, F. & Hance, A. J. Science
300, 1112 (2003).
11. Klarmann, G. J., Chen, X., North, T. W. & Preston, B. D.
J. Biol. Chem. 278, 7902–7909 (2003).
12. Chaudhuri, J. et al. Nature 422, 726–730 (2003).
13. Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F.
Proc. Natl Acad. Sci. USA 100, 4102–4107 (2003).
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Planetary science
The history of air
H. J. Melosh
Giant impacts on Earth destroyed the envelope of gases surrounding the
fledgling planet — so how has the modern-day planet regained its
atmosphere? The answer, it seems, is that all was not lost.
he Earth was born in violence. Modern
scenarios of its origin suggest that, as
the Earth grew, matter arrived in progressively larger chunks. The final crescendo
included the impact of a Mars-size protoplanet that added mass and energy to the
nascent Earth and, incidentally, created the
Moon. So great was the energy delivered in
this impact that the proto-Earth probably
melted completely, and silicate vapour
formed a fiery (although short-lived) envelope around the planet. Amidst such hostility, it seems hardly possible that the fragile
envelope of atmospheric gases could survive.
Planetary scientists have taken it virtually for
granted that the primordial atmosphere of
the proto-Earth would have been stripped by
such a stupendous impact, and have looked
for mechanisms that might have regenerated
the gaseous envelope after the tumult subsided. But Genda and Abe have taken a closer
look at the problem and, writing in Icarus1,
they show that Earth’s atmosphere is not
quite as fragile as it once seemed.
The idea that impacts of kilometre-size
comets or asteroids might strip off a small
fraction of a terrestrial planet’s atmosphere
has been discussed for many years (for
example, see ref. 2). In these relatively small
events, the atmosphere in the vicinity of the
impact is driven off by the high-speed
vapour and debris that are ejected from the
crater3. For planet-size impactors, however,
the loss mechanism is different. Of course,
T
the atmosphere close to the impact site will
be ejected with the other high-speed gases
from the vaporized projectile. But, because
the depth of the atmosphere is only a small
fraction of the Earth’s radius, this kind of
direct stripping cannot remove the atmosphere that lies far from the impact site.
Instead, a planetary-scale impact creates a
strong shock wave in the Earth’s mantle that
propagates through its dense interior and
emerges as a sudden jump in surface velocity
at locations far from the impact site. If the
velocity jump is big enough, a further shock
wave forms that may accelerate the atmosphere to a high enough velocity for it to
escape the Earth.
Chen and Ahrens4 were the first to analyse
this global atmospheric ejection process.
They assumed that the velocity of the motion
generated at the surface reaches 8 km s11
and found that, at this velocity, most of
the atmosphere is ejected. Genda and Abe1
used a one-dimensional atmosphere model
similar to that of Chen and Ahrens, but they
benefited from more recent giant-impact
modelling that shows that the actual surface
velocities following a Mars-size impact are
smaller than those assumed by Chen and
Ahrens. According to such computations5,
the maximum surface velocities only reach
about 6 km s11 at the antipode of the impact
and are smaller elsewhere. The difference in
velocity between 6 and 8 km s11 may sound
trivial, but it corresponds to a steep step in
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© 2003 Nature Publishing Group