Good to CU Yapeng Gu and Wesley I

news and views Good to CU 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 original RNA), is synthesized. The resulting the bacterium Escherichia coli9. Thus it was virus to multiply in otherwise resis- double-stranded DNA is incorporated into suggested that APOBEC3G might inhibit Htant human cells1–3. This protein, Vif the host-cell genome, and, when switched HIV replication by altering the coding capa- — for ‘viral infectivity factor’ — works by on, is used to generate the proteins and RNA city of viral RNA or DNA4. overcoming a cellular protein, APOBEC3G, needed to form new virus particles (virions). Harris et al.5, Mangeat et al.6 and Zhang whose task is to inhibit the replication It has been known for more than a decade et al.7 have now shown that APOBEC3G of HIV and other retroviruses4. As they that the Vif protein is required for HIV to can indeed alter the sequences of the HIV describe in Cell 5 and on pages 94 and 99 of replicate in some human cell types (termed and other retroviral genomes, producing an this issue6,7, three groups have now discov- ‘non-permissive’ cells), but not others exceptionally high frequency of guanine- ered how APOBEC3G hampers viral repli- (‘permissive’ cells)1–3. Non-permissive cells to-adenosine (G-to-A) substitutions in the cation. The authors find that, as the express APOBEC3G (also known as CEM15), plus (protein-coding) strand of the viral retroviral RNA genome is copied into DNA and permissive cells become non-permissive DNA.As shown in detail in Fig.1,this obser- in host cells, this protein changes ‘C’s to ‘U’s upon expression of this protein4. These and vation implies that APOBEC3G changes C’s in the DNA. APOBEC3G therefore repre- other data indicate that APOBEC3G blocks to U’s in the DNA minus strand during sents a remarkable innate cellular defence viral replication, and that Vif works by over- replication (because,when the plus strand is mechanism that drastically alters the chem- coming this block. However, the precise made using the minus strand as a template, ical composition and coding capacity of nature of the replication block has not been G’s are inserted opposite C’s, but A’s oppo- replicating retroviruses. clear — and it is unusual in that it is manifest site U’s). Importantly, G-to-A hypermuta- Retroviruses, which include HIV and after the virus has entered a new target cell.So, tion is suppressed by the presence of murine leukaemia virus (MLV), have Vif-deficient viruses produced by non-per- Vif 5–7,10, and APOBEC3G has the required genomes that are made up of single-stranded missive cells are released at normal levels,but deaminase activity5,7 and can act on single- RNA. For these viruses to replicate in a host are somehow impaired in their ability to form stranded DNA substrates5. Deamination cell, a double-stranded DNA copy of the stable, productive replication intermediates by APOBEC3G is quite promiscuous, but RNA genome must be made, by the process when they enter new target cells3,8. exhibits some sequence selectivity, with a of reverse transcription.This happens in two Clues to how this might happen have preference for C/T–C–C sequences5–7. steps.First,a DNA strand that has a sequence come from several observations. First, Conversion of C’s to U’s in the genomic complementary to the RNA is produced APOBEC3G can be packaged into HIV-1 DNA minus strand apparently blocks viral (this is called ‘minus-strand’DNA).Then the virions4. Second, APOBEC3G is related to a replication in several ways (Fig. 1). First, the RNA is removed and a second (plus-strand) family of enzymes that catalyse the deamina- presence of uracils can target the minus DNA molecule, complementary to the first tion of cytosine bases (C’s) in DNA and strand for destruction.Uracil is not normally (and therefore matching the sequence of the RNA, thereby producing uracils (U’s). found in DNA and can therefore be excised Finally, APOBEC3G can mutate the DNA of by host DNA-repair enzymes. This could

Target cell

Uracil-DNA glycosylase APOBEC3G ′ Minus-strand DNA (–) Destruction 5 (–) ? ′ Vif Strand breakage Vif 3 ? RNA 5′ primers Plus-strand DNA ReverseReverse G C U synthesis impaired transcriptiontranscription APOBEC3G (+)(–) Second- 3′5′ tRNA G G C U strand G Infection G C synthesis G Deamination U A U G-to-A hypermutation V NH2 Genomic ′ O RNA Viral RNA 3 3′ A U 5′ N HN A U O O N O N O 5′ O P O O P O O O 3′ O H H O H H H H H H Plus-strand O H O H editing and repair? 2′-deoxycytidine 2′-deoxyuridine Figure 1 Editing HIV: how the cellular APOBEC3G protein might inhibit the minus strand, producing 2፱-deoxyuridines (U). Plus-strand synthesis HIV replication5–7,10. From left, APOBEC3G has been packaged, together then converts these C-to-U changes into G-to-A mutations, because C pairs with the viral genome, in a viral particle. Then, when the retrovirus enters with G, whereas U pairs with A. C-to-U conversion can diminish HIV-1 a new cell, the viral reverse transcriptase copies the genomic RNA into a replication in several ways: deglycosylation of uracil can lead to strand double-stranded DNA. Replication begins at a tRNA primer (purple), and breakage and destruction; the presence of U’s can reduce plus-strand creates first a DNA minus (ǁ) strand that is a complementary copy of the synthesis11; and G-to-A hypermutations in the viral genome can impair all RNA, and then a DNA plus (+) strand that is a complementary copy of the subsequent viral functions. The viral Vif protein blocks the effects of minus strand. However, APOBEC3G deaminates 2፱-deoxycytidines (C) in APOBEC3G through an as yet undefined mechanism.

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© 2003 Nature Publishing Group news and views eventually lead to strand breakage and tools with which to study innate cellular 3. Gabuzda, D. H. et al. J. Virol. 66, 6489–6495 (1992). destruction — explaining the apparent immune systems,because the battle between 4. Sheehy, A. M., Gaddis, N. C., Choi, J. D. & Malim, M. H. Nature 418, 646–650 (2002). instability of viral reverse transcripts. Sec- cells and retroviruses is an ancient and 5. Harris, R. S. et al. Cell 113, 803–809 (2003). ond, uracils in the minus strand can impair intense one — as exemplified by the fact that 6. Mangeat, B. et al. Nature 424, 99–102 (2003). the initiation of plus-strand synthesis during retroviral elements make up an astonishing 7. Zhang, H. et al. Nature 424, 94–98 (2003). HIV-1 reverse transcription11. Finally, even 8% of the human genome15. Other cellular 8. von Schwedler, U., Song, J., Aiken, C. & Trono, D. J. Virol. 67, 4945–4955 (1993). when complete, double-stranded DNA defences against retroviruses include ZAP, a 9. Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. Mol. Cell copies of the viral genome are made, they protein that targets viral messenger RNAs for 10, 1247–1253 (2002). contain many G-to-A mutations, which destruction16, and Fv-1 (and related cellular 10.Lecossier, D., Bouchonnet, F., Clavel, F. & Hance, A. J. Science result in amino-acid changes and aberrant proteins), which inhibits early stages of 300, 1112 (2003). 17,18 11.Klarmann, G. J., Chen, X., North, T. W. & Preston, B. D. ‘stop’ signals in the encoded proteins, and retroviral replication . The molecular J. Biol. Chem. 278, 7902–7909 (2003). 5–7,10 generally reduce viral fitness at every sub- description of APOBEC3G activity has 12.Chaudhuri, J. et al. Nature 422, 726–730 (2003). sequent stage in replication6. The biased G- revealed yet another arm of the innate 13.Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F. to-A mutation profile might also explain the immune system, in which cells actually edit Proc. Natl Acad. Sci. USA 100, 4102–4107 (2003). ■ 14.Mehta, A., Banerjee, S. & Driscoll, D. M. J. Biol. Chem. 271, overall A-richness of the HIV-1 genome, as the genomes of invading retroviruses. 28294–28299 (1996). well as the non-lethal hypermutation some- Yapeng Gu and Wesley I. Sundquist are in the 15.International Human Genome Sequencing Consortium Nature 5–7,10 times observed during viral replication . Department of Biochemistry, University of Utah, 409, 860–921 (2001). As with all other immune responses, Salt Lake City, Utah 84132, USA. 16.Gao, G., Guo, X. & Goff, S. P. Science 297, 1703–1706 (2002). 17.Best, S., Le Tissier, P., Towers, G. & Stoye, J. P. Nature 382, e-mail: [email protected] APOBEC3G must successfully distinguish 826–829 (1996). between ‘self’ and ‘non-self’.So it is remark- 1. Fisher, A. G. et al. Science 237, 888–893 (1987). 18.Hatziioannou, T., Cowan, S., Goff, S. P., Bieniasz, P. D. able that, as two of the groups show, the pro- 2. Strebel, K. et al. Nature 328, 728–730 (1987). & Towers,G.J.EMBO J. 22, 385–394 (2003). tein can inhibit the infectivity of retroviruses that differ markedly in sequence, including MLV5,6, simian immunodeficiency virus, Planetary science equine infectious anaemia virus (EIAV), and even engineered retroviruses — derived from HIV-1 — that contain little of the original The history of air genome6. Presumably, these genomes are H. J. Melosh specifically targeted because APOBEC3G is incorporated into virus particles, and/or Giant impacts on Earth destroyed the envelope of gases surrounding the because only virus-specific intermediates are fledgling planet — so how has the modern-day planet regained its selected for deamination. It will therefore atmosphere? The answer, it seems, is that all was not lost. be important to learn how APOBEC3G is packaged into virions, and how it selects its he Earth was born in violence. Modern the atmosphere close to the impact site will substrates. Intriguingly, another member of scenarios of its origin suggest that, as be ejected with the other high-speed gases this enzyme family,AID (activation-induced Tthe Earth grew, matter arrived in pro- from the vaporized projectile. But, because cytidine deaminase), which is involved in gressively larger chunks. The final crescendo the depth of the atmosphere is only a small antibody-gene diversification, also targets included the impact of a Mars-size proto- fraction of the Earth’s radius, this kind of single-stranded DNA. It requires transcrip- planet that added mass and energy to the direct stripping cannot remove the atmos- tion of the targeted gene into RNA12,13, and nascent Earth and, incidentally, created the phere that lies far from the impact site. the presence of an RNA-degrading enzyme13. Moon. So great was the energy delivered in Instead, a planetary-scale impact creates a By analogy, APOBEC3G might target single- this impact that the proto-Earth probably strong shock wave in the Earth’s mantle that stranded minus DNA after reverse transcrip- melted completely, and silicate vapour propagates through its dense interior and tion and removal of the RNA template by formed a fiery (although short-lived) enve- emerges as a sudden jump in surface velocity the RNA-degrading activity of the reverse lope around the planet. Amidst such hostili- at locations far from the impact site. If the transcriptase enzyme.Alternatively, substrate ty, it seems hardly possible that the fragile velocity jump is big enough, a further shock targeting could be mediated by a cofactor, as envelope of atmospheric gases could survive. wave forms that may accelerate the atmos- is the case for another family member14. Planetary scientists have taken it virtually for phere to a high enough velocity for it to Another issue, which could have thera- granted that the primordial atmosphere of escape the Earth. peutic implications, is how Vif overcomes the proto-Earth would have been stripped by Chen and Ahrens4 were the first to analyse the antiviral activity of APOBEC3G. Possibi- such a stupendous impact, and have looked this global atmospheric ejection process. lities include downregulation of APOBEC3G for mechanisms that might have regenerated They assumed that the velocity of the motion protein levels, exclusion of the protein from the gaseous envelope after the tumult sub- generated at the surface reaches 8 km sǁ1 progeny virions, and inactivation of incor- sided.But Genda and Abe have taken a closer and found that, at this velocity, most of porated APOBEC3G molecules4.Moreover, look at the problem and, writing in Icarus1, the atmosphere is ejected. Genda and Abe1 do viruses such as MLV and EIAV, which they show that Earth’s atmosphere is not used a one-dimensional atmosphere model do not have the Vif gene, avoid the effects quite as fragile as it once seemed. similar to that of Chen and Ahrens, but they of APOBEC3G by expressing other pro- The idea that impacts of kilometre-size benefited from more recent giant-impact teins with Vif-like activities? Or do they comets or asteroids might strip off a small modelling that shows that the actual surface simply replicate only in host cells that lack fraction of a terrestrial planet’s atmosphere velocities following a Mars-size impact are APOBEC3G? has been discussed for many years (for smaller than those assumed by Chen and It is becoming increasingly apparent that example, see ref. 2). In these relatively small Ahrens. According to such computations5, cells have evolved a remarkable number of events, the atmosphere in the vicinity of the the maximum surface velocities only reach mechanisms to defend themselves from impact is driven off by the high-speed about 6 km sǁ1 at the antipode of the impact microbial invaders, and that microbes have vapour and debris that are ejected from the and are smaller elsewhere. The difference in discovered clever ways to circumvent those crater3. For planet-size impactors, however, velocity between 6 and 8 km sǁ1 may sound defences. Retroviruses are particularly good the loss mechanism is different. Of course, trivial, but it corresponds to a steep step in

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