The HIV-1 life cycle, that very approximately lasts one day in normal conditions, can be split into an early and a late phase of replication. The early steps begin with the attachment of the virion at the cell surface, and finish with the integration of the proviral DNA into the host genome. The succeeding late part of the viral replication extends until virion release.
Once the infection is initiated, the HIV-1 particle travels, mainly in the blood, lymph or lymphatic tissues, until it attaches to the cell surface of its target cells, thanks to low-specificity interactions between the virus and one amongst a long list of cellular proteins. These target cells are resting or activated CD4+ T lymphocytes and macrophages, which are non-dividing immune cells that also express CD4. The subsequent Env conformational switch that allows the gp41-mediated, pHindependent, fusion of the viral and cellular membranes is triggered by an interaction between gp120 and its CD4 receptor and either the CXCR4 or CCR5 co-receptor (Doms and Trono, 2000; Saphire et al., 2000). HIV-1 strains that use CXCR4 as a co-receptor are named X4 strains, while the ones using CCR5 are named R5 strains. X4 strains usually emerge only late during the course of a human infection, and are often associated with progression to AIDS (Scarlatti et al., 1997).
The consequence of this membrane fusion is the shedding of the matrix shell followed by the release of the viral core into the “receiver” cell. The genomic RNA is then reverse transcribed into a linear double-stranded DNA molecule (Freed and Martin, 2001). This process, which is mediated by the viral RT, begins with the elongation of a cellular tRNALys, which serves as a primer, and involves the degradation of the viral RNA template by the RT RNase H activity.
The structural end product of the reverse transcription process, called the “preintegration complex” (PIC), is imported into the nucleus. The precise mechanisms that permit this active transport are still a matter of intense debate.
Although the enzymatic integration reaction per se is well understood and can be recapitulated in vitro with purified integrase (Esposito and Craigie, 1999), very little is known about the series of events occurring between the PIC nuclear entry and the integration in the context of the nucleus, and more particularly in the context of higher order chromatin. Chromatin-remodeling factors might play a role during these steps (Farnet and Bushman, 1997; Kalpana et al., 1994), and might be responsible for the HIV-1 preferential integration in active transcriptional units in human cells (Schroder et al., 2002). Furthermore, the chromatin status at the integration locus also influences postintegration stages, namely the basal expression level of the provirus and, more importantly, its putative latency (Jordan et al., 2003; Jordan et al., 2001).
The stably integrated HIV-1 provirus, a 10 kb long DNA molecule, serves as a template for the transcription of viral messengers and genomic RNA by the cellular Pol II polymerase (Freed and Martin, 2001). The viral promoter, which functions in a broad array of cells is situated in the U3 part of the 5’ LTR and requires activation by cellular trancription factors, including NF-κB and NFAT. The initial transcriptional output is however very low, due to the blocked elongation of viral transcripts early in the 5’ portion of the RNAs. The viral transactivator protein Tat, which is made very early from the tiny amounts of successfully terminated mRNAs, is required to achieve normal levels of expression (Jeang et al., 1999). The binding of Tat to the stem-loop trans-acting response element (TAR) present on HIV-1 RNAs 5’ R region indeed results in a marked increase of transcriptional processivity (Greene and Peterlin, 2002). This effect is mediated by the phosphorylation of the PolII tail by the Tatrecruited cellular positive transcription elongation factor pTEFb, which is composed of the cyclin T1 and the CDK9 kinase. Thereafter, full length HIV-1 transcripts are efficiently synthesized. These are transported to the cytoplasm either unspliced (genomic RNA, which also serves as the Gag and Gag- Pol mRNA), partially spliced (encoding Vif, Vpr, Vpu and Env) or fully spliced (encoding Tat, Rev and Nef). A system of alternative splicing allows the provirus to produce this large series of mRNAs as well as the full length genomic RNA from a relatively short DNA sequence (Freed and Martin, 2001). The viral Rev protein indeed ensures that unspliced and partially spliced mRNAs, that still contain functional splice sites, manage to exit the nucleus, which is normally forbidden (Greene and Peterlin, 2002). For that task, Rev bridges the incompletely spliced and unspliced viral RNAs to the export machinery, by binding both to the cellular export factor Crm1 and to the viral RNA RRE cisactingelements. Accordingly, the fact that Rev is encoded from a fully spliced mRNA allows the initial export and translation of its mRNA.
The same genomic-length unspliced mRNA drives the expression of the structural and enzymatic polyproteins precursors Gag and Gag-Pol, the production of the later arising through a ribosomal frameshift that occurs in about 5% of the cases (Freed, 1998). Both precursors multimerize through interactions of different domains along Gag and are targeted by myristoylation of their N terminus matrix domain to the inner leaflet of the plasma membrane, where they concentrate in lipid rafts that putatively serve as assembly platforms (Bukrinskaya, 2004). In parallel, the trimeric integral viral glycoprotein envelope (Env) is recruited through interactions with matrix. Moreover, two copies of the viral genomic RNA are recruited through the binding of their stem loops packaging signal, which is located just downstream of the 5’ LTR, to the zinc fingers present in the NC domain of Gag. NC-RNA interactions are also involved in the tight assembly of Gag and Gag-Pol (Freed and Martin, 2001). The accumulation of 1500 to 2000 densely packed viral polyproteins beneath the plasma membrane induces its curvature and then the formation of a membrane-coated spherical particle, still linked to the cell by a stem-like structure (Goff, 2001). The late domain of the HIV-1 p6 part of Gag mediates the final viral pinching off by recruiting at the budding site the cellular Tsg101 protein and several associated factors. These, which are components of the cellular vesicular sorting pathway (VPS) (Garrus et al., 2001), are normally involved in the budding of cellular vesicles into the lumen of late endosomes, a mechanism that topologically parallels the final steps of HIV-1 virion release. The newly released particles have a so-called immature morphology, characterized by a thick layer of radially arranged Gag and Gag-Pol precursors. During or shortly after the budding is finished, the viral protease is auto-activated and cleaves both Gag and Gag-Pol precursors into their sub-components. As a consequence, these reorganize from an “assembly mode” configuration to a “target cell attack” configuration harboring the characteristic conical inner cores