Structure and genome of HIV
The genome and proteins of HIV have been the subject of extensive research in the twenty years since the discovery of the virus.
Structure
HIV is different in structure from previously described retroviruses. It is around 120 nm in diameter (120 billionths of a meter; around 60 times smaller than a red blood cell) and roughly spherical.
HIV-1 is composed of two copies of single-stranded RNA enclosed by a conical capsid comprising the viral protein p24, typical of lentiviruses (Figure 1). This is in turn surrounded by a plasma membrane of host-cell origin. The single-strand RNA is tightly bound to the nucleocapsid proteins, p7 and enzymes that are indispensable for the development of the virion, such as reverse transcriptase and integrase. The nucleocapsid (p7 and p6) associates with the genomic RNA (one molecule per hexamer) and protects the RNA from digestion by nucleases. A matrix composed of an association of the viral protein p17 surrounds the capsid, ensuring the integrity of the virion particle. Also enclosed within the virion particle are Vif, Vpr, Nef, p7 and viral protease (Figure 1). The envelope is formed when the capsid buds from the host protein, taking some of the host-cell membrane with it. The envelope includes the glycoproteins gp120 and gp41.
Genome organisation
HIV has several major genes coding for structural proteins that are found in all retroviruses, and several nonstructural ("accessory") genes that are unique to HIV. The gag gene provides the basic physical infrastructure of the virus, and pol provides the basic mechanism by which retroviruses reproduce, while the others help HIV to enter the host cell and enhance its reproduction. Though they may be altered by mutation, all of these genes except tev exist in all known variants of HIV; see Genetic variability of HIV.
- gag (Group-specific Antigen): codes for p24, the viral capsid; p6 and p7, the nucleocapsid proteins; and p17, a matrix protein.
- pol: Codes for viral enzymes, the most important of which are reverse transcriptase, integrase, and protease which cleaves the proteins derived from gag and pol into functional proteins.
- env (for "envelope"): Codes for the precursor to gp120 and gp41, proteins embedded in the viral envelope which enable the virus to attach to and fuse with target cells.
- tat, rev, nef, vif, vpr, vpu: Each of these genes codes for a single protein with the same names; see Tat, Rev, Nef, Vif, Vpr, Vpu.
- tev: This gene is only present in a few HIV-1 isolates. It is a fusion of parts of the tat, env, and rev genes, and codes for a protein with some of the properties of Tat, but little or none of the properties of Rev.
Protein function
p24, p6, p7, p17
These proteins are encoded by the gag gene, and provide structural elements of the virus: p24 makes up the viral capsid, p6 and p7 provide the nucleocapsid, and p17 provides a protective matrix.
When a Western blot test is used to detect HIV infection, p24 is one of the three major proteins tested for, along with gp120/gp160 and gp41.
Reverse transcriptase
Common to all retroviruses, this enzyme transcribes the viral RNA into double-stranded DNA.
Integrase
This enzyme integrates the DNA produced by reverse transcriptase into the host's genome.
Protease
A protease is any enzyme that cuts proteins into segments. HIV's gag and pol genes do not produce their proteins in their final form, but as larger combination proteins; the specific protease used by HIV cleaves these into separate functional units. Protease inhibitor drugs block this step.
gp120
Exposed on the surface of the viral envelope, the glycoprotein gp120 binds to the CD4 receptor on any target cell that has such a receptor, particularly the helper T-cell. See HIV tropism and Life cycle of HIV.
Since CD4 receptor binding is the most obvious step in HIV infection, gp120 was among the first targets of HIV vaccine research. These efforts have been hampered by its chemical properties, which make it difficult for antibodies to bind to gp120; also, it can easily be shed from the virus due to its loose binding with gp41.
gp41
The glycoprotein gp41 is non-covalently bound to gp120, and provides the second step by which HIV enters the cell. It is originally buried within the viral envelope, but when gp120 binds to a CD4 receptor, gp120 changes its conformation causing gp41 to become exposed, where it can assist in fusion with the host cell.
Fusion inhibitor drugs such as enfuvirtide block the fusion process by binding to gp41.
The env gene does not actually code for gp120 and gp41, but for a precursor to both, gp160. During HIV reproduction, the host cell's own enzymes cleave gp160 into gp120 and gp41. See Life cycle of HIV.
Tat
Stands for "Trans-Activator of Transcription". Tat consists of between 86 and 101 amino acids depending on the subtype (Jeang, 1996; Campbell et al., 2005). The HIV RNA initially has a hairpin-structured portion which prevents full transcription occurring. However, a small number of RNA transcripts will be made, which allow the Tat protein to be produced. Tat binds to and phosphorylates cellular factors, eliminating the effect of the hairpin RNA structure and allowing transcription of the HIV DNA (Kim, 2001). This itself increases the rate of transcription, providing a positive feedback cycle. This in turn allows HIV to have an explosive response once a threshold amount of Tat is produced, a useful tool for defeating the body's response. Despite the lack of a signal sequence, Tat is released by infected cells and is found in detectable levels (more than 40nM) in the culture supernatants of cells infected with HIV-1, and in the sera of HIV-1 infected patient’s (Xiao, 2000). It is also efficiently taken up by a variety of HIV-1 uninfected cells. Extracellular Tat has many functions that are thought to play a major role in enabling HIV to escape immune surveillance and to act as a viral toxin in AIDS pathology. One such role of Tat is in the apoptosis of uninfected naive bystander T cells, contributing to the progressive loss of these cells and the progression towards AIDS (Campbell et al., 2004).
Rev
Stands for "Regulator of Virion". This protein allows fragments of HIV mRNA that contain a Rev Response Unit (RRE) to be exported from the nucleus to the cytoplasm. In the absence of the rev gene, RNA splicing machinery in the nucleus quickly splices the RNA so that only the smaller, regulatory proteins can be produced; in the presence of rev, RNA is exported from the nucleus before it can be spliced, so that the structural proteins and RNA genome can be produced. Again, this mechanism allows a positive feedback loop to allow HIV to overwhelm the host's defenses, and provides time-dependant regulation of replication (a common process in viral infections) (Strebel, 2003).
Nef
Stands for "Negative Regulatory Factor". The expression of Nef early in the viral life cycle ensures T cell activation and the establishment of a persistent state of infection, two basic attributes of HIV infection. Nef also promotes the survival of infected cells by downmodulating the expression of several surface molecules important in host immune function. These include major histocompatibility complex-I (MHC I) and MHC II present on antigen presenting cells (APCs) and target cells, and CD4 and CD28 present on CD4+ T cells. One group of patients in Sydney were infected with a nef-deleted virus and took much longer than expected to progress to AIDS (Learmont et al., 1999). A nef-deleted virus vaccine has not been trialed in humans and has failed in nonhuman animals.
Vif
Stands for "Viral Infectivity Factor". Vif, a 23-kilodalton protein, Vif, is essential for viral replication, though its exact role is as yet unclear (Strebel, 2003). However, it is thought that vif helps the virus to infect other cells after it leaves a host cell. Vif appears to be involved in determining how the RNA genome and Gag protein bind to each other, and inhibits a cellular protein that modifies RNA.
Vpr
Stands for "Viral Protein R". Vpr, a 10-kilodalton protein, plays an important role in regulating nuclear import of the HIV-1 pre-integration complex, and is required for virus replication in non-dividing cells. Vpr also induces cell cycle arrest in proliferating cells, which can result in immune dysfunction (Bukrinsky et al., 1999).
Vpu
Stands for "Viral Protein U". Vpu is involved in viral budding, enhancing virion release from the cell. In HIV-2, the vpu gene is called vpx.
References
- Bukrinsky M, Adzhubei A. (1999) Viral protein R of HIV-1. Rev Med Virol 9, 39-49 PMID 10371671
- Campbell GR, Pasquier E, Watkins J, Bourgarel-Rey V, Peyrot V, Esquieu D, Barbier P, de Mareuil J, Braguer D, Kaleebu P, Yirrell DL, Loret EP. (2004) The glutamine-rich region of the HIV-1 Tat protein is involved in T-cell apoptosis. J. Biol. Chem. 279, 48197-48204 PMID 15331610
- Campbell GR, Watkins JD, Esquieu D, Pasquier E, Loret EP and Spector SA (2005) The C-terminus of HIV-1 Tat modulates the extent of CD178 mediated apoptosis of T cells. J. Biol. Chem. In Press. PMID 16155003
- Gelderblom, H. R. (1997) Fine structure of HIV and SIV. In: Los Alamos National Laboratory (Ed) HIV Sequence Compendium, 31-44.
- Jeang, K. T. (1996) In: Human Retroviruses and AIDS: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos National Laboratory (Ed.) pp. III-3–III-18
- Kim JB, Sharp PA. (2001) Positive transcription elongation factor B phosphorylates hSPT5 and RNA polymerase II carboxyl-terminal domain independently of cyclin-dependent kinase-activating kinase. J. Biol. Chem. 276, 12317-12323 PMID 11145967
- Learmont JC, Geczy AF, Mills J, Ashton LJ, Raynes-Greenow CH, Garsia RJ, Dyer WB, McIntyre L, Oelrichs RB, Rhodes DI, Deacon NJ, Sullivan JS. (1999) Immunologic and virologic status after 14 to 18 years of infection with an attenuated strain of HIV-1. A report from the Sydney Blood Bank Cohort. N Engl J Med 340, 1715-1722 PMID 10352163
- Strebel, K (2003) Virus-host interactions: role of HIV proteins Vif, Tat, and Rev. AIDS 17 Suppl 4, S25-S34 PMID 15080177
- Xiao, H., Neuveut, C., Tiffany, H. L., Benkirane, M., Rich, E. A., Murphy, P. M. and Jeang, K. T. (2000) Selective CXCR4 antagonism by Tat: implications for in vivo expansion of coreceptor use by HIV-1. Proc. Natl. Acad. Sci. U. S. A. 97, 11466-11471 PMID 11027346