Lentiviral genomes

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Lentiviral genomes

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HIV and host factors References
Lentiviral genetic maps. A) HIV-1 strain HXB2. B) HIV-2 BEN. C) A representative simian immunodeficiency virus, SIV Sykes. The image is based on diagrams from the Los Alamos HIV Compendium. A great variety of HIV sequences and analysis of their function can be found at the Los Alamos collection of HIV databases.

            Some representative genetic maps of lentiviral proviruses are shown in Figure 3.  The lentiviruses comprise a broad genus within the retroviruses that are related by the sequences of their nucleic acids and proteins, which in turn program the interactions of viral proteins with each other and with proteins of the host.  The top map shows a representative HIV-1, the strain HXB2, which is one of the first cloned and studied.  Defining the left and right edges of the genome are the long terminal repeats, or LTRs.  The LTRs contain cis acting sites important for integration and starting and stopping transcription. 

            Proceeding rightward, the first reading frame encountered is gag, which encodes the p17 (MA), p24 (CA), and p7 (NC), as well as some smaller peptides such as p6.

            Right of gag is the pol coding region, which encodes protease (PR), p51 (RT), p15 (RNAaseH), and p31 (IN).  The mature reverse transcriptase is a heterodimer of p51 and p66, the latter a fusion of p51 and p15.  Overlapping the C-terminal IN coding region is the vif gene, followed by vpr and vpu.  The env region encodes gp120 and gp41.  The tat and rev genes are comprised of two exons overlapping env.  Rightward of these and partially overlapping is the nef gene, which also overlaps the 3' or right LTR. 

            Below the HIV-1 genome map are shown the HIV-2 genome and a representative SIV, that from Sykes monkeys (SIVsykes).  For each the reading frames show varying degrees of homology to their HIV counter parts, and each contains a different complement of auxillary genes.  HIV-2 contains an extra gene, termed vpx, that is important for programming degradation of a cellular restriction factor.  SIVsykes lacks both vpx and vpr.  In each genome, the various genes are distributed in different arrangements over the three reading frames (indicated by the rows containing the genes).  Thus lentiviruses show conserved features against a background of individual variation.