Structure and genome of HIV
The genome and proteins of HIV (human immunodeficiency virus) have been the subject of extensive research since the discovery of the virus in 1983. 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 was not until two years after the first major cases of AIDS associated illnesses were reported in 1981.
HIV-1 is composed of two copies of non-covalently linked positive single-stranded RNA enclosed by a conical capsid comprising the viral protein p24, typical of lentiviruses (Figure 1). Lysine tRNA is the primer of the Magnesium dependent, reverse transcriptase. It packages two copies of its positive strand, unspliced, 5'guanosine-capped and 3'-polyadenylated RNA genome which is used for strand-transfer-mediated recombination which enables the virus to rapidly evolve under stress or pressure from the environment. The RNA component is 9749 nucleotides long. RNA genome has a 5’ cap (Gppp), a 3’ poly(A)tail, and many open reading frames (ORFs). Viral structural proteins are encoded by long ORFs, whereas smaller ORFs encode regulators of viral life cycle comprising attachment, membrane fusion, replication, and assembly. This is in turn surrounded by an envelope of host-cell origin. The single-strand RNA is tightly bound to the nucleocapsid proteins, p6, 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 cell, taking some of the host-cell membrane with it. The envelope includes the glycoproteins gp120 and gp41.
As a result of its role in virus-cell attachment, the structure of the virus envelope spike, consisting of gp120 and gp41, is of particular importance. It is hoped that determining the envelope spike's structure will contribute to scientific understanding of the virus and its replication cycle, and help in the creation of a cure. The first model of its structure was compiled in 2006 using cryo-electron tomography and suggested that each spike consists of a trimer of three gp120–gp41 heterodimers. However, published shortly after was evidence for a single-stalk "mushroom" model, with a head consisting of a trimer gp120s and a gp41 stem, which appears as a compact structure with no obvious separation between the three monomers, anchoring it to the envelope. There are various possibilities as to the source of this difference, as it is unlikely that the viruses imaged by the two groups were structurally different. More recently, further evidence backing up the heterodimer trimer-based model has been found.
Genome organization 
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. HIV has three major genes, 5'gag-pol-env-3', encoding major structural proteins as well as essential enzymes. These are synthesized as polyproteins which produce proteins for virion interior, called Gag, group specific antigen; the viral enzymes (Pol, polymerase) or the glycoproteins of the virion env (envelope). In addition to these, HIV encodes for proteins which have certain regulatory and auxiliary functions as well. HIV-1 has two important regulatory elements: Tat and Rev and few important accessory proteins such as Nef, Vpr, Vif and Vpu which are not essential for replication in certain tissues. 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):encodes for the precursor gag polyprotein, which is processed by viral protease during maturation to MA (matrix protein, p17); CA (capsid protein, p24); SP1 (spacer peptide 1, p2); NC (nucleocapsid protein, p7); SP2 (spacer peptide 2, p1) and p6.
- pol: encodes for viral enzymes reverse transcriptase(RT) and RNase H, integrase (IN), and HIV protease (PR). HIV protease is required to cleave the precursor gag polyprotein to produce structural proteins, RT required to transcribe DNA from RNA template as well as IN to integrate the ds viral DNA into the host genome.
- env (for "envelope"): codes for gp160, which is cleaved by cellular protease rather than viral to produce the surface (SU) lipoprotein gp120(SU)which attaches to the CD4 receptors present on lymphocytes and gp41(transmembrane, TM), proteins embedded in the viral envelope that enable the virus to attach to and fuse with target cells.
- Essential regulatory elements: Tat and Rev
- Tat- HIV trans-activator(Tat)plays an important role in regulating the reverse transcription of viral genome RNA ensuring efficient synthesis of viral mRNAs as well as regulating the release of the virions from the infected cells. Tat is expressed as 72-amino acid one-exon Tat as well as the 86-101 amino-acid two-exon Tat playing an important role early in HIV infection.Tat(14-15kDa) binds to the bulged genomic RNA stem-loop secondary structure near the 5' LTR region forming the Tat Responsive element (TAR).
- [[Regulator of expression of Virion proteins (Rev): The Rev protein binds to an arginine rich RNA-binding motif of the viral genome which acts as NLS (nuclear localization signals), required for the transport of Rev to the nucleus from cytosol during viral replication. Rev recognizes a complex stem-loop structure of the mRNA env located in the intron separating coding exon of Tat and Rev which is known as the Rev response element (RRE). Rev is important for the synthesis of major viral proteins, hence essential for viral replication.
- Accessory regulatory proteins: Nef, Vpr, Vif and Vpu.
- "The lentivirus protein R (vpr): Vpr is a virion-associated, nucleocytoplasmic shuttling regulatory protein. It is believed to play an important role in replication of the virus. It is believed to play an important role in nuclear import of preintegration complex as well as inducing arrest in G2 of cycling cells which activates the DNA repair machinery which could be used by the virus for the integration of the viral DNA. HIV-2 and SIV encode an additional Vpr related protein called Vpx which functions sin association with Vpr.
- vif,- Vif is a highly conserved, 23 kDa phosphoprotein important for the infectivity of HIV-1 virions depending on the cell-type. Some cells such as lymphocytes, macrophages, and cell lines like H9 cells require Vif for synthesis of fully infectious viruses where as other cells such as Hela, Cos and others do not require Vif.
- nef- Nef, negative factor, is a N-terminal myristoylated membrane-associated phosphoprotein. It is involved in multiple functions during the replication cycle of the virus. It is believed to play an important role in cell apoptosis and increase in virus infectivity.
- vpu,Virus protein U- Vpu is specific to HIV-1, is a class I oligomeric integral membrane phosphoprotein with numerous biological functions. It is involved in the CD4 degradation involving the ubiquitin proteasome pathway as well as in the successful release of the virions from the infected cells.
- 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.
HIV employs a sophisticated system of differential RNA splicing to obtain nine different gene products from a less than 10kb genome. HIV has a 9.2kb unspliced genomic transcript which encodes for gag and pol precursors; a singly spliced, 4.5 kb encoding for env, Vif, Vpr and Vpu and a multiply spliced mRNA,2kb encoding for Tat, Rev and Nef.
RNA secondary structure 
|HIV pol-1 stem loop|
|Predicted secondary structure of the HIV pol-1 stem loop|
Several conserved secondary structure elements have been identified within the HIV RNA genome. The 5'UTR structure consists of series of stem-loop structures connected by small linkers. These stem-loops (5' to 3') include the trans-activation region (TAR) element, the 5' polyadenylation signal [poly(A)], the PBS, the DIS, the major SD and the ψ hairpin structure located within the 5' end of the genome and the HIV Rev response element (RRE) within the env gene. Another RNA structure that has been identified is gag stem loop 3 (GSL3), thought to be involved in viral packaging. RNA secondary structures have been proposed to affect the HIV life cycle by altering the function of HIV protease and reverse transcriptase, although not all elements identified have been assigned a function.
An RNA secondary structure determined by SHAPE analysis has shown to contain three stem loops and is located between the HIV protease and reverse transcriptase genes. This cis regulatory RNA has been shown to be conserved throughout the HIV family and is thought to influence the viral life cycle.
The complete structure of an HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution.
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- Rfam entry for HIV pol-1 stem loop