**3. Organization of viral genome**

The majority of replication competent retroviruses depend on three genes: "group specificantigen" (*gag*), "polymerase" (*pol*) and "envelope"(*env*) genes. The "classic" structure of a retroviral genome is: 5'LTR-*gag*-*pol*-*env*-LTR 3 ' (Figure 2). The non-coding LTR ('long terminal repeat") represents the two ends of the viral genome and they are linked to host cell DNA after integration. The *gag* and *env* genes encode the core and the viral envelope glycoproteins respectively. The *pol* gene encodes for the RT, IN and protease [13]. In addition, HIV contains in its 9.749 kb RNA, six additional genes: *vif, vpu* (only in HIV-1)*, vpr, vpx* (only in HIV-2), *tat, rev, and nef*) which contribute to their genetic complexity and helps virus in several steps during replication cycle [14].

**Figure 2. HIV-1 genome organization**. The major viral proteins encoded by *gag*, *pol* and *env* genes are indicated in red. Numbers indicate the beginning and ending of each gene according to nucleotide numbering of HXB2CG HIV-1 strain (GenBank accession number: K03455).

The *vif* gene codes for Vif, a protein that increases the infectivity of the HIV particle. This protein is found inside HIV-infected cells, and its main function is to interfere with one of the innate immune system's defenses - a cellular protein called APOBEC3G [15].

where the reverse transcription takes place (4). The RTC transforms to the preintegration complex (PIC), composed by several cellular and viral components, that is imported to the nucleus where viral DNA is integrated into cellular chro‐ mosomal DNA (5 and 6). The proviral DNA is then transcribed (7) and mRNA migrates to the cytoplasm and translat‐ ed to viral proteins (8). Assembly of different components of viral particles occurs at plasma membrane (9). After egress and release of immature virions (10), the proteolytical cleavage of Gag polyprotein takes place leading to ma‐

78 Trends in Basic and Therapeutic Options in HIV Infection - Towards a Functional Cure

After replication, transcription and translation, the viral genome information is ready to proceed to the final step: the viral assembly, the release and maturation of recently formed virions. The nucleocapsid assembly occurs through protein-protein interactions mediated by the uncleaved Gag polyprotein – through the capsid (CA) domain [10] – that also recruits the viral genomic RNA, through the interaction between the nucleocapsid (NC) domain and the RNA packaging signal (*Psi* sequence) [11]. The NC domain also mediates the formation of the RNA dimer via a palindromic sequence in the dimer linkage structure (DLS) sequence, which is located in the *Psi* sequence. In addition, specific cellular tRNAs are packaged. The assembly of the virus particle, which final steps occur at the plasma membrane (reviewed in [12]), is partly regulated by the Vpu and Vif proteins, which play an important role in the assembly of the virus. At the cell membrane, the immature viruses are released and maturation takes place through polypeptide cleavage mediated by the viral protease. The mature virus is now able

The majority of replication competent retroviruses depend on three genes: "group specificantigen" (*gag*), "polymerase" (*pol*) and "envelope"(*env*) genes. The "classic" structure of a retroviral genome is: 5'LTR-*gag*-*pol*-*env*-LTR 3 ' (Figure 2). The non-coding LTR ('long terminal repeat") represents the two ends of the viral genome and they are linked to host cell DNA after integration. The *gag* and *env* genes encode the core and the viral envelope glycoproteins respectively. The *pol* gene encodes for the RT, IN and protease [13]. In addition, HIV contains in its 9.749 kb RNA, six additional genes: *vif, vpu* (only in HIV-1)*, vpr, vpx* (only in HIV-2), *tat, rev, and nef*) which contribute to their genetic complexity and helps virus in several steps during

**Figure 2. HIV-1 genome organization**. The major viral proteins encoded by *gag*, *pol* and *env* genes are indicated in red. Numbers indicate the beginning and ending of each gene according to nucleotide numbering of HXB2CG HIV-1 strain

ture virions (11).

to infect other cells.

replication cycle [14].

(GenBank accession number: K03455).

**3. Organization of viral genome**

The "Viral protein U", (coded by *vpu* gene), enhances the release of new viral particles, helping them to bud from the host cell. Vpu also works within the infected cell to enhance the degra‐ dation of CD4 protein. This has the effect of reducing the amount of CD4 present in plasma membrane, therefore reducing the likelihood of superinfection [16].

The "Viral protein R", (coded by *vpr* gene), is incorporated into viral particles through a specific interaction with Gag proteins. It has several functions during intracellular steps of viral replication. For instance, Vpr is present in the PIC and has been shown to influence the reverse transcription and the nuclear import of viral DNA; it also modulates cell cycle progression and apoptosis of infected cell [17].

Tat and Rev are regulatory proteins coded by *tat* and *rev* genes. They are present in the nucleus of infected cells and bind to defined regions of the viral DNA and RNA. These proteins enhances the transcription of proviral DNA into mRNA, promote the RNA elongation, stimulate the transport of HIV-1 mRNA from the nucleus to the cytoplasm and also are essential for translation [9].

Tat is a regulatory transactivator protein, which enhances the activation of HIV long terminal repeat (LTR) increasing the efficiency of HIV genomic transcription. This enhancement is also the result of additional interaction between Tat and cellular transcription factors such as NFκB and SP-1. Furthermore, Tat also plays a crucial role in AIDS pathogenesis, especially in the development of HIV-associated dementia, dysregulation of cytokine expression and induction of apoptosis [9]. As referred earlier in this chapter, Rev facilitates the nuclear export of singlespliced and unspliced viral mRNAs (~4 kb and ~9 kb mRNAs respectively). The molecular mechanism underlying Rev activity involves a direct interaction between Rev protein and a *cis*-acting sequence-specific target named RRE (Rev-responsive element). RRE is found within the *env* gene in all incompletely spliced mRNAs [9, 18]. It has been shown that Nef protein has several functions. It induces down-regulation of CD4 [19] and the HLA class I and II molecules from the surface of HIV infected cells [20], which may represent an important escape mecha‐ nism for the virus to avoid recognition by CD4+ T cells. Nef may also interfere with T cell activation, as a result of selective binding to various proteins that are involved in intracellular signaling [21].
