APOBEC3G

Last updated
APOBEC3G
Protein APOBEC3G PDB 2JYW.png
Available structures
PDB Human UniProt search: PDBe RCSB
Identifiers
Aliases APOBEC3G , A3G, ARCD, ARP-9, ARP9, CEM-15, CEM15, MDS019, bK150C2.7, dJ494G10.1, apolipoprotein B mRNA editing enzyme catalytic subunit 3G
External IDs OMIM: 607113 HomoloGene: 128348 GeneCards: APOBEC3G
Orthologs
SpeciesHumanMouse
Entrez

60489

n/a

Ensembl

ENSG00000239713

n/a

UniProt

Q9HC16

n/a

RefSeq (mRNA)

NM_021822

n/a

RefSeq (protein)

NP_068594
NP_001336365
NP_001336366
NP_001336367

n/a

Location (UCSC)n/an/a
PubMed search [1] n/a
Wikidata
View/Edit Human

APOBEC3G (apolipoprotein B mRNA editing enzyme, catalytic subunit 3G) is a human enzyme encoded by the APOBEC3G gene that belongs to the APOBEC superfamily of proteins. [2] This family of proteins has been suggested to play an important role in innate anti-viral immunity. [3] APOBEC3G belongs to the family of cytidine deaminases that catalyze the deamination of cytidine to uridine in the single stranded DNA substrate. [2] The C-terminal domain of A3G renders catalytic activity, several NMR and crystal structures explain the substrate specificity and catalytic activity. [4] [5] [6] [7] [8] [9] [10] [11]

APOBEC3G exerts innate antiretroviral immune activity against retroviruses, most notably HIV, by interfering with proper replication. However, lentiviruses such as HIV have evolved the Viral infectivity factor (Vif) protein in order to counteract this effect. Vif interacts with APOBEC3G and triggers the ubiquitination and degradation of APOBEC3G via the proteasomal pathway. [12] On the other hand, foamy viruses produce an accessory protein Bet ( P89873 ) that impairs the cytoplasmic solubility of APOBEC3G. [13] The two ways of inhibition are distinct from each other, but they can replace each other in vivo. [14]

Discovery

It was first identified by Jarmuz et al. [15] as a member of family of proteins APOBEC3A to 3G on chromosome 22 in 2002 and later also as a cellular factor able to restrict replication of HIV-1 lacking the viral accessory protein Vif. Soon after, it was shown that APOBEC3G belonged to a family of proteins grouped together due to their homology with the cytidine deaminase APOBEC1.

Structure


APOBEC3G has a symmetric structure, resulting in 2 homologous catalytic domains, the N-terminal (CD1) and C-terminal (CD2) domains, each of which contains a Zn2+
 coordination site. [16] Each domain also has the typical His/Cys-X-Glu-X23–28-Pro-Cys-X2-Cys motif for cytidine deaminases. However, unlike the typical cytidine deaminases, APOBEC3G contains a unique alpha helix between two beta sheets in the catalytic domain that could be a cofactor binding site. [17] (Figure 1)

CD2 is catalytically active and vital for deamination and motif specificity. CD1 is catalytically inactive, but very important for binding to DNA and RNA and is key to defining the 5’->3’ processivity of APOBEC3G deamination. [18] CD2 has no deaminase activity without the presence of CD1. [19]

Native APOBEC3G is composed of monomers, dimers, trimers, tetramers, and higher order oligomers. While it is thought that APOBEC3G functions as a dimer, it is possible that it actually functions as a mix of monomers and oligomers. [18]

The D128 amino acid residue, which lies within CD1 (Figure 1), appears to be particularly important for APOBEC3G interactions with Vif because a D128K point mutation prevents Vif-dependent depletion of APOBEC3G. [20] [21] Additionally, amino acids 128–130 on APOBEC3G form a negatively charged motif that is critical for interactions with Vif and the formation of APOBEC3G-Vif complexes. Furthermore, residues 124-127 are important for encapsidation of APOBEC3G into HIV-1 virions and the resulting antiretroviral activity. [22]

Mechanism of action

APOBEC3G has been widely studied and several mechanisms that negatively affect HIV-1 replication have been identified.

Cytidine deamination and hypermutation

APOBEC3G and other proteins in the same family are able to act as activation-induced (cytidine) deaminases (AID). APOBEC3G interferes with reverse transcription by inducing numerous deoxycytidine to deoxyuridine mutations in the negative strand of the HIV DNA primarily expressed as complementary DNA (cDNA) [12] in a 3’->5’processive manner. [23] Because APOBEC3G is part of the APOBEC superfamily and acts as an AID, it is likely that the mechanism mediated by APOBEC3G for cytidine deamination is similar to that of an E. coli cytidine deaminase that is known to be highly homologous to APOBEC1 and AID around the nucleotide and zinc-binding region. The predicted deamination reaction is driven by a direct nucleophilic attack on position 4 of the cytidine pyrimidine ring by the zinc-coordinated enzyme. Water is needed as a source of both a proton and hydroxyl group donor (Figure 2). [24] The deamination (and resulting oxidation) at position 4 yields a carbonyl group and results in a change from cytidine to uridine.

The deamination activity ultimately results in G→A hypermutations at “hot spots” of the proviral DNA. Such hypermutation ultimately destroys the coding and replicative capacity of the virus, resulting in many nonviable virions. [12] [25] APOBEC3G has a much weaker antiviral effect when its active site has been mutated to the point that the protein can no longer mutate retroviral DNA. [26] It was originally thought that the APOBEC3G-mediated deamination can also indirectly lead to viral DNA degradation by DNA repair systems attracted to the mutated residues. [27] However, this has been discounted because human APOBEC3G reduces viral cDNA levels independently of DNA repair enzymes UNG and SMUG1. [28]

Interference with reverse transcription

APOBEC3G interferes with reverse transcription of HIV-1 independent of DNA deamination. tRNA3Lys typically binds to the HIV-1 primer binding site to initiate reverse transcription. APOBEC3G can inhibit tRNA3Lys priming, thereby negatively affecting viral ssDNA production and virus infectivity. [27] It is predicted that reverse transcription is also negatively affected by APOBEC3G binding to viral RNA and causing steric alterations. [16]

Interference with viral DNA integration

APOBEC3G was associated with interference of viral DNA integration into the host genome in a manner dependent on functional catalytic domains and deaminase activity. Mbisa et al. saw that APOBEC3G interferes with the processing and removal of primer tRNA from the DNA minus strand, thus leading to aberrant viral 3’ long terminal repeat (LTR) DNA ends. These viral DNA ends are inefficient substrates for integration and plus-strand DNA transfer. As a result, HIV-1 provirus formation is inhibited. [23]

Biological function

HIV encapsidation

Figure 3: Four proposed mechanisms of APOBEC3G encapsidation in HIV-1 virions. The mechanisms involving interaction with viral RNA and interaction with Gag proteins have been extensively confirmed. Mechanisms of encapsidation.png
Figure 3: Four proposed mechanisms of APOBEC3G encapsidation in HIV-1 virions. The mechanisms involving interaction with viral RNA and interaction with Gag proteins have been extensively confirmed.

APOBEC3G mRNA is expressed in certain cells, referred to as non-permissive cells, in which HIV-1 cannot properly infect and replicate in the absence of Vif. Such cells include physiologically relevant primary CD4 T lymphocytes and macrophages. [30] The encapsidation of APOBEC3G into HIV-1 virions is very important for the spread of APOBEC3G and the exertion of anti-retroviral activity. Encapsidation of APOBEC3G may occur by at least the following four proposed mechanisms (Figure 3): 1. Non-specific packaging of APOBEC3G 2. APOBEC3G interaction with host RNA 3. APOBEC3G interaction with viral RNA 4. Interaction of APOBEC3G with HIV-1 Gag proteins. Only the latter two mechanisms have been extensively supported. [29]

The amount that is incorporated into virions is dependent on the level of APOBEC3G expression within the cell producing the virion. Xu et al. conducted studies with PBMC cells and found that, in the absence of Vif, 7±4 APOBEC3G molecules were incorporated into the virions and resulted in potent inhibition of HIV-1 replication. [31]

In addition to deterring replication of exogenous retroviruses, A3G also acts upon human endogenous retroviruses, leaving similar signatures of hypermutations in them. [32] [33]

Disease relevance

APOBEC3G is expressed within the non-permissive cells and is a key inhibitory factor of HIV-1 replication and infectivity. However, Vif counteracts this antiretroviral factor, enabling production of viable and infective HIV-1 virions in the presence of APOBEC3G activity . [30] [34] In particular, Vif prevents incorporation of APOBEC3G into HIV-1 virions and promotes destruction of the enzyme in a manner independent of all other HIV-1 proteins. [35]

While APOBEC3G has typically been studied as a vital protein exhibiting potent antiviral effects on HIV-1, recent studies have elucidated the potential of APOBEC3G-mediated mutation to help to facilitate the propagation HIV-1. The number of deaminations in the preferred regions varies from one to many, possibly dependent on the time of exposure to APOBEC3G. [25] Additionally, it has been shown that there is a dose response between intracellular APOBEC3G concentration and degree of viral hypermutation. [36] Some HIV-1 proviruses with APOBEC3G-mediated mutation have been shown to thrive because they carry too few mutations at APOBEC3G hotspots or because recombination between a lethally APOBEC3G-restricted provirus and a viable provirus has occurred. [37] Such sublethal mutagenesis contributes to greater genetic diversity among the HIV-1 virus population, demonstrating the potential for APOBEC3G to enhance HIV-1's ability to adapt and propagate.

Related Research Articles

Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases.

<i>Rhabdoviridae</i> Family of viruses in the order Mononegavirales

Rhabdoviridae is a family of negative-strand RNA viruses in the order Mononegavirales. Vertebrates, invertebrates, plants, fungi and protozoans serve as natural hosts. Diseases associated with member viruses include rabies encephalitis caused by the rabies virus, and flu-like symptoms in humans caused by vesiculoviruses. The name is derived from Ancient Greek rhabdos, meaning rod, referring to the shape of the viral particles. The family has 40 genera, most assigned to three subfamilies.

The genome and proteins of HIV have been the subject of extensive research since the discovery of the virus in 1983. "In the search for the causative agent, it was initially believed that the virus was a form of the Human T-cell leukemia virus (HTLV), which was known at the time to affect the human immune system and cause certain leukemias. However, researchers at the Pasteur Institute in Paris isolated a previously unknown and genetically distinct retrovirus in patients with AIDS which was later named HIV." Each virion comprises a viral envelope and associated matrix enclosing a capsid, which itself encloses two copies of the single-stranded RNA genome and several enzymes. The discovery of the virus itself occurred two years following the report of the first major cases of AIDS-associated illnesses.

<span class="mw-page-title-main">Viral infectivity factor</span>

Viral infectivity factor, or Vif, is an accessory protein found in HIV and other lentiviruses. Its role is to disrupt the antiviral activity of the human enzyme APOBEC by targeting it for ubiquitination and cellular degradation. APOBEC is a cytidine deaminase enzyme that mutates viral nucleic acids.

<span class="mw-page-title-main">ADAR</span> Mammalian protein found in Homo sapiens

The double-stranded RNA-specific adenosine deaminase enzyme family are encoded by the ADAR family genes. ADAR stands for adenosine deaminase acting on RNA. This article focuses on the ADAR proteins; This article details the evolutionary history, structure, function, mechanisms and importance of all proteins within this family.

<span class="mw-page-title-main">PSME4</span> Protein found in humans

Proteasome activator complex subunit 4 is a protein that in humans is encoded by the PSME4 gene.

<span class="mw-page-title-main">APOBEC1</span>

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 also known as C->U-editing enzyme APOBEC-1 is a protein that in humans is encoded by the APOBEC1 gene.

<span class="mw-page-title-main">APOBEC3F</span>

DNA dC->dU-editing enzyme APOBEC-3F is a protein that in humans is encoded by the APOBEC3F gene.

<span class="mw-page-title-main">APOBEC3C</span> Protein-coding gene in humans

DNA dC->dU-editing enzyme APOBEC-3C is a protein that in humans is encoded by the APOBEC3C gene.

<span class="mw-page-title-main">APOBEC3A</span>

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A, also known as APOBEC3A, or A3A is a gene of the APOBEC3 family found in humans, non-human primates, and some other mammals. It is a single-domain DNA cytidine deaminase with antiviral effects. While other members of the family such as APOBEC3G are believed to act by editing ssDNA by removing an amino group from cytosine in DNA, introducing a cytosine to uracil change which can ultimately lead to a cytosine to thymine mutation, one study suggests that APOBEC3A can inhibit parvoviruses by another mechanism. The cellular function of APOBEC3A is likely to be the destruction of foreign DNA through extensive deamination of cytosine.Stenglein MD, Burns MB, Li M, Lengyel J, Harris RS. "APOBEC3 proteins mediate the clearance of foreign DNA from human cells". Nature Structural & Molecular Biology. 17 (2): 222–9. doi:10.1038/nsmb.1744. PMC 2921484. PMID 20062055.

<span class="mw-page-title-main">APOBEC3B</span>

Probable DNA dC->dU-editing enzyme APOBEC-3B is a protein that in humans is encoded by the APOBEC3B gene.

<span class="mw-page-title-main">APOBEC3D</span>

Probable DNA dC->dU-editing enzyme APOBEC-3D is a protein that in humans is encoded by the APOBEC3D gene.

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<span class="mw-page-title-main">APOBEC</span> Enzyme involved in messenger RNA editing

APOBEC is a family of evolutionarily conserved cytidine deaminases.

<span class="mw-page-title-main">APOBEC3H</span>

DNA dC->dU-editing enzyme APOBEC-3H, also known as Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3H or APOBEC-related protein 10, is a protein that in humans is encoded by the APOBEC3H gene.

<span class="mw-page-title-main">APOBEC4</span> Protein-coding gene in the species Homo sapiens

C->U-editing enzyme APOBEC-4, also known as Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 4, is a protein that in humans is encoded by the APOBEC4 gene. It is primarily expressed in testis and found in mammals, chicken, but not fishes.

<span class="mw-page-title-main">Kataegis</span>

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Viviana Simon is a Professor of Microbiology at the Icahn School of Medicine at Mount Sinai (ISMMS). She is a member of the ISMMS Global Health and Emerging Pathogens Institute. Her research considers viral-host interactions and the mode of action of retroviral restriction factors. During the COVID-19 pandemic, Simon developed an antibody test that can determine immunity to Coronavirus disease 2019.

References

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  32. ↑ Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, et al. (September 2008). "Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences". Journal of Virology. 82 (17): 8743–61. doi:10.1128/JVI.00584-08. PMC   2519685 . PMID   18562517.
  33. ↑ Lee YN, Malim MH, Bieniasz PD (September 2008). "Hypermutation of an ancient human retrovirus by APOBEC3G". Journal of Virology. 82 (17): 8762–70. doi:10.1128/JVI.00751-08. PMC   2519637 . PMID   18562521.
  34. ↑ Goncalves J, Santa-Marta M (September 2004). "HIV-1 Vif and APOBEC3G: multiple roads to one goal". Retrovirology. 1 (28): 28. doi:10.1186/1742-4690-1-28. PMC   521195 . PMID   15383144.
  35. ↑ Stopak K, de Noronha C, Yonemoto W, Greene WC (September 2003). "HIV-1 Vif blocks the antiviral activity of APOBEC3G by impairing both its translation and intracellular stability". Molecular Cell. 12 (3): 591–601. doi: 10.1016/S1097-2765(03)00353-8 . PMID   14527406.
  36. ↑ Pillai SK, Wong JK, Barbour JD (March 2008). "Turning up the volume on mutational pressure: is more of a good thing always better? (A case study of HIV-1 Vif and APOBEC3)". Retrovirology. 5 (26): 26. doi:10.1186/1742-4690-5-26. PMC   2323022 . PMID   18339206.
  37. ↑ Mulder LC, Harari A, Simon V (April 2008). "Cytidine deamination induced HIV-1 drug resistance". Proceedings of the National Academy of Sciences of the United States of America. 105 (14): 5501–6. Bibcode:2008PNAS..105.5501M. doi: 10.1073/pnas.0710190105 . PMC   2291111 . PMID   18391217.

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