HIVs genome is 9'8 KB, and encodes 2 other classes of proteins besides the usual GAGPOLENV proteins'

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HIVs genome is 9.8 KB, and encodes 2 other
classes of proteins besides the usual GAG-POL-ENV
proteins.
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HIV gene expression is mainly from integrated
provirus and is separated temporally into early
genes and late genes.
Late gene expression requires Rev. RRE is the
binding site for Rev in the unspliced and
partially spliced RNA. Unspliced RNA is
incorporated into virions (genome).
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Activating Transcription of the HIV genome.
The LTR promoter contains binding sites for
several cellular transcription factors, including
(common) SP1 and TBP factors, but also NF-kappa
B. The activity of NF-kappa B is inducible, and
is regulated by several external signals that
stimulate T cells.
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Tat binds to the TAR RNA domain, and stimulates
transcription by promoting elongation (i.e.,
promoter clearance) by RNAP II. The Tat-RNA
complex promotes phosphorylation of the CTD of
RNAP II by recruiting kinases that catalyze
phosphorylation.
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Infection Cycle
Tat, nef and rev genes expressed early.
Gag, Pol and Env genes expressed late.
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Infection gp120 and gp41 associate with one
another. The complete complex is trimeric (3
copies of each protein). Beta turns in C3 and C4
regions are important for binding to the
cell-surface CD4 receptor.
Primary Target CD4 helper T cells. The normal
role of these cells is to stimulate macrophages
to destroy pathogens, coordinate the immune
response. They have on their surface, a
glycoprotein called CD4. The viral protein gp120
binds CD4. Gp120 also binds the chemokine
co-receptor. gp41 causes membrane fusion (between
virion and cell).
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Co-receptors for HIV
Chemokine receptor family CCR5, CXC, CXCR4,
CCR2b CD4 is necessary but not sufficient for
HIV entry into CD4 T-lymphocytes. The chemokine
receptors act as co-receptors.
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Why is the disease less aggressive in some
people? Mutations in chemokine co-receptors that
confer resistance.
CCR5 polymorphism
- About 1 of Caucasians are resistant to the
virions - 32 bp deletion in this gene (second
extracellular loop) - these people can still get
HIV from variants that can use the CXCR4
co-receptor.
CXCR4 3' UTR mutation
- 1 Caucasians - delays the onset and the
time of death. - point mutation in the 3' UTR.
Mechanism unknown.
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Current Therapies

• Nucleoside analogues and other RT inhibitors
• Active site inhibitors of the HIV protease
• Interferon (stimulated anti-viral response
• Cocktails of all 3.

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Nucleoside analogues
Inhibit at the reverse transcriptase step by
causing chain termination. The trick is to find
one that the HIV reverse transcriptase accepts
readily, but the host's DNA polymerases tend to
reject.
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Vaccines?
Whole virus vaccines Attenuated viruses
Essentially intact, living HIV virions that have
been chemically or genetically damaged. Whole
killed virus Intact virions that have been
damaged so badly that they are completely
nonfunctional (dead). Subunit vaccines Clone
one gene from HIV, express the protein and use it
to vaccinate patients. The disadvantage is that
the person only raises antibodies against one
target. In the free virus, the only target are
the envelope proteins. However, these are
extremely variable proteins. Six amino acids of
the V3 loop of gp120 appear to be relatively
constant. Some variability exists but most
antibodies cross react with the variants.
Antibodies against cocktails of different V3's
are being tried. Nucleic Acid Vaccines
Gene gun, muscle expression.
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A Major Challenge in Maintaining Control of HIV

• HIV evolves rapidly
• The RT is error-prone (no proof-reading)
• 1-2 mutations in each cDNA copy of the 9.8 kb
  RNA genome