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NAME: JULIE KILEY

REG NO. B132/12031/2015

COURSE : MICROBIOLOGY AND BIOTECHNOLOGY.

UNIT NAME: VIROLOGY.

UNIT CODE: SZL 315.

INTRODUCTION.

HIV GENETICS
The genes of HIV are located in the central region of the proviral DNA and is encoded on one
long strand of RNA. (In a free virus particle, there are actually two separate strands of RNA, but
they’re exactly the same). When the virus is integrated into the host’s DNA genome (as a
provirus) then its information too is encoded in DNA. The HIV genome is approximately 9.8
kilobases in length. Both ends of the provirus are flanked by a repeated sequence known as the
long terminal repeats (LTRs).

The following are the genes in HIV genome:

The major structural proteins are:-

· gag (coding for the viral capsid proteins).

· pol (notably, coding for reverse transcriptase)

(NB. gag and pol together can be expressed in one long strand called “gag-pol“.

· env (coding for HIV’s envelope-associated proteins).

The regulatory proteins, Tat and Rev.

The accessory proteins, Vpu, Vpr, Vif, and Nef.

The HIV genome also has a “Long Terminal Repeat” (LTR) at each end of its genome – not
quite a gene, but a sequence of RNA/DNA which is the same at either end and which serves
some structural and regulatory purposes.
DISCUSSION.
gag.

gag is one of the three “main” genes found in all retroviruses. It contains around 1500
nucleotides, and encodes four separate proteins which form the building blocks for the viral core:

Capsid protein. p24 is the core protein in the HIV virus particle. It forms the "capsid" of the
virus, the case in which HIV's RNA genome is kept. The level of p24 found in the blood serum is
an indicator of HIV progression (and similarly, a dropping level of antibodies to p24).

Matrix protein. p17 serves a structural function inside mature HIV particles. Units of p17 line
the inside of the HIV envelope, helping to anchor the gp41/gp120 "spikes" to the envelope. Once
the HIV core has entered the cell, p17 also serves the function of helping it be transferred into
the cell's nucleus. It achieves this because it carries "nuclear localisation signals" (sequences of
protein which are recognised by cellular machinery as indicating that it should be transported
into the nucleus).

Nucleocapsid protein. The nucleocapsid protein p9 binds to HIV's genomic RNA, and holds it
in place in the virus core.

p6. The protein p6, one of the products of the gag gene, helps vpr to be incorporated into newly-
made virus particles.

The most significant role of the gag gene is therefore to encode important proteins which will
make up the viral core.

pol.

pol is one of the main retroviral genes. It encodes four proteins, of which the most important is
Reverse Transcriptase. Reverse Transcriptase performs a job which is unique to retroviruses, in
that it copies the virus’ RNA genome into DNA. (Since most organisms and viruses keep their
genes in DNA form in the first place, they have no need to perform this task.) The copying of the
HIV genome into DNA form is one of the key stages of the HIV life-cycle. The other three
products of pol are these:

· Protease – which processes proteins made from HIV’s genome so that they can become
part of new fully-functioning HIV particles

· RNAse H – which breaks down the retroviral genome following infection of a cell

· Integrase – which integrates the DNA copy of HIV’s genome into the host DNA

env.
The “env” gene in HIV encodes a single protein, gp160. (When gp160 is synthesised in the cell,
cellular enzymes add complex carbohydrates and turn it from a protein into a glycoprotein –
hence the name “gp160″ rather than “p160″.)

gp160 travels to the cell surface, where cellular enzymes again attack it, this time chopping into
two pieces – gp120, and gp41. If and when new virus particles bud off from the host cell, these
two pieces lie on opposite sides of the virus membrane. gp120 sits on the outside of the virus
particle, forming the virus’s spikes, while gp41 sits just on the inside of the membrane – each
gp41 being anchored to a gp120 through the membrane.

tat.

“Tat” is short for “transactivator” – it’s a regulatory gene which accelerates the production of
more HIV virus. In fact, it’s crucial to HIV, because HIV completely fails to replicate itself
without it. Tat protein is also toxic, so the large amounts of tat protein released into the blood by
HIV-infected cells are no help for the body.

Tat works because the protein encoded by tat binds to the start of a new HIV RNAstrand – a part
which has been called the “Transactivator Active Region” orTAR. The TAR runs from +1 to
+59, that is to say, the first 59 nucleotides of the HIV genome. Once the cellular machinery has
transcribed this much provirus into RNA, tat can bind to it and encourage the transcription of the
remainder of the HIV genetic code.

rev.

“rev” is another of HIV’s regulator genes. It stimulates the production of HIV proteins, but
suppresses the expression of HIV’s regulatory genes. The messenger RNAs of HIV can either be
sent to the protein-producing part of the cell intact, or they can have bits cut out of them first
(splicing). The intact mRNA tends to encode HIV proteins (such as envelope and capsid
proteins), while the spliced mRNA encodes regulatory genes such as tat and nef.

So the rev help intact to mRNA to be exported from the cell nucleus. It binds to the mRNA at a
specific point (the Rev-Responsive Element), and this complex of RNA and rev is sent out of the
nucleus. A molecule of rev can “shuttle” in and out of the nucleus, potentially taking a new set of
RNA out each time it leaves the nucleus.

nef.

The “negative replication factor” (“nef”) gene encodes a protein which hangs around in the
cytoplasm of the cell, and retards HIV replication. it does this by modifying cellular proteins that
regulate the initiation of transcription – that is, it affects the proteins which tell the cell whether
or not to make RNAcopies of the DNAcode.

vif.
The “vif” gene codes for “virion infectivity factor”, a protein that increases the infectivity of the
HIV particle. The protein is found inside HIV-infected cells, and it works by interfering with one
of the immune system’s defences – a cellular protein called APOBEC3G. vif sticks to
APOBEC3G and encourages the cell to degrade it, preventing it doing its job of sneaking into
newly-formed virus particles and making them non-productive. This has been verified in
experiments. If you can create a HIV virus with the Vif protein missing (we would call this a
“delta-Vif” strain of HIV), then it can still infect a cell – but the new virus particles produced
from that cell contain APOBEC3G and therefore aren’t very effective at infecting other cells.

vpr.

“Viral protein R” accelerates the production of HIV proteins. It also facilitates the nuclear
localisation of the pre-integration complex – the agglomeration of viral RNA and reverse
transcriptase and integrase proteins which must form in order for the HIV genome to be
integrated into the host cell’s genome. Vpr carries “nuclear localisation signals” (sequences of
protein which are recognised by cellular machinery as indicating that it should be transported
into the nucleus), and in a sense, it mimics the behaviour of a protein called importin-beta.

The other role for Vpr is stopping the host cell going through the ordinary “cell cycle” – many
cells normally go through a regular cycle of splitting to create new cells, but Vpr can stop host
cells doing this. It seems that a cell which has been stopped during the so-called “G2″ phase of
the cell cycle is a nicer environment for HIV replication.

There are 100 copies of this protein in every HIV virion. The cellular protein cyclophilin A is
important for the production of Vpr.

vpu.

“Viral protein U” helps with the assembly of new virus particles, and helps them to bud from the
host cell. It’s possible for HIV to replicate and bud without this particular protein, but only 10%
or 20% as many new virus particles are produced.

Vpu also works within the infected cell to enhace the degradation of CD4 proteins. This has the
effect of reducing the amount of CD4 sticking out of the infected cell, therefore reducing the
likelihood of superinfection. Without the vpu gene, HIV virus actually kills its host cell quicker!
A secondary effect of vpu is to delay the cytopathic (cell-killing) effects of virus infection,
keeping the cell alive slightly longer so that it can produce more virus particles.

vpx.

vpx is found in HIV-2 (and SIV), but not in HIV-1. It is closely related to vpr (if we compare
their genetic sequences), which indicates that its existence might have come about as a
duplication of the vpr gene.
Its role in the life of HIV is not entirely clear! It certainly seems to be “dispensable”, since types
of HIV-2 without a functioning vpx gene still seem to be able to replicate and to infect cell.
However, it seems that vpx does have some effect of making viral reproduction more efficient,
especially in non-dividing cells such as macrophages. The molecular mechanisms behind this are
not yet fully understood.

Long Terminal Repeat.

The Long Terminal Repeat is something which is often found in strands of RNA or DNA is the
Long Terminal Repeat. At each end of the string is the same sequence of code at each end of the
string. Almost like the repeat at the start and finish of these sentences,

There are two important functions for the LTR:

· Firstly they are “sticky ends” which the integrase protein uses to insert the HIV genome
into host DNA.

· Secondly, they act as promoter/enhancers – when integrated into the host genome, they
influence the cell machinery which transcribes DNA, to alter the amount of transcription which
occurs. Protein binding sites in the LTR are involved with RNA initiation.

Protein synthesis of an HIV-genome.

Reverse transcription

In reverse transcription, viral RNA is "reverse transcribed" into DNA. This process, catalysed by
reverse transcriptase enzymes, that allows retroviruses, including the human immunodeficiency
virus (HIV), to use RNA as their genetic material. Without reverse transcriptase, the viral
genome couldn't become incorporated into the host cell, and couldn't reproduce.

Reverse transcriptase sometimes makes mistakes reading the RNA sequence. The result is that
not all viruses produced in a single infected cell are alike. Instead, they end up with a variety of
subtle molecular differences in their surface coat and enzymes.

Translation

The mRNA formed in transcription is transported out of the nucleus, into the cytoplasm, to the
ribosome. Here, it directs protein synthesis. Messenger RNA is not directly involved in protein
synthesis − transfer RNA (tRNA) is required for this. The process by which mRNA directs
protein synthesis with the assistance of tRNA is called translation.
The ribosome is a very large complex of RNA and protein molecules. Each three-base stretch of
mRNA (triplet) is known as a codon, and one codon contains the information for a specific
amino acid. As the mRNA passes through the ribosome, each codon interacts with the anticodon
of a specific transfer RNA (tRNA) molecule by Watson-Crick base pairing. This tRNA molecule
carries an amino acid at its 3′-terminus, which is incorporated into the growing protein chain.
The tRNA is then expelled from the ribosome.

Each amino acid has its own special tRNA. For example, the tRNA for histidine (tRNAHis) is
different from that for phenylalanine (tRNAPhe). Each amino acid is attached to its tRNA
through the 3′-OH group to form an ester which reacts with the α-amino group of the terminal
amino-acid of the growing protein chain to form a new amide bond (peptide bond) during protein
synthesis. The reaction of esters with amines is generally favourable but the rate of reaction is
increased greatly in the ribosome.

Each transfer RNA molecule has a well-defined tertiary structure that is recognized by the
enzyme aminoacyl tRNA synthetase, which adds the correct amino acid to the 3′-end of the
uncharged tRNA. The presence of modified nucleosides is important in stabilizing the tRNA
structure.

Assembly, Budding and Maturation of HIV Virions.

Assembly. The process by which viral proteins and nucleic acids come together in an infected
cell to produce new virus particles. The path to virus assembly begins with synthesis of the Gag
polyprotein in the cytosol and its translocation to the site of assembly. During its trafficking to
the plasma membrane, or after its arrival there, Gag interacts with dimeric viral RNA. Virus
assembly proceeds at the plasma membrane, and viral Env glycoproteins accumulate at the site.
Gag then recruits the cellular ESCRT machinery (Box 1), which drives the membrane scission
reaction required for particle release.

On reaching the plasma membrane, Gag induces the recruitment and coalescence of cholesterol-
and sphingolipid-enriched membrane microdomains, often referred to as lipid rafts. The targeting
of Gag to lipid rafts in the plasma membrane and the importance of PtdIns(4,5 P2 in this plasma
membrane targeting are reflected by the high levels of cholesterol, sphingolipid and
PtdIns(4,5)P2 that are found on the viral membrane. Lipid rafts probably serve as platforms for
virus assembly, and the targeting of Gag to these microdomains may facilitate the incorporation
of Env glycoproteins into virions. Given that areas of cell–cell contact — referred to by
virologists as 'virological synapses' — are also rich in lipid rafts, the preference exhibited by Gag
for lipid raft-like membrane microdomains may enhance assembly at the virological synapse,
thereby promoting cell–cell viral transfer.

RNA encapsidation. After synthesis in the nucleus, HIV-1 RNAs are transported to the
cytoplasm, where they undergo two main processes: translation into viral proteins and packaging
into newly assembled virus particles. A large number of viral mRNA species are synthesized,
some of which are multiply spliced before nuclear export; others largely escape splicing and are
exported in a partially spliced or unspliced form. Export of intron-containing viral RNAs is
mediated by a highly structured cis-acting RNA element known as the Rev-responsive element
(RRE), which is bound by the virus-encoded trans-acting protein Rev. Rev, which shuttles
between the nucleus and the cytoplasm, promotes nuclear export by forming a complex with the
nuclear export factor CRM1 (also known as EXP1) and the GTPase RAN.

As is the case for other retroviruses, two copies of full-length viral RNA are packaged into HIV-
1 virions. The presence of two copies of genomic RNA in each particle provides the opportunity
for recombination during reverse transcription and may also allow reverse transcription to
proceed if one RNA copy is damaged. The bulk of recent evidence suggests that RNA
dimerization occurs in the cytosol or at the plasma membrane and that an RNA dimer is the
recognition unit for packaging into assembling virions.

After assembly of the immature Gag lattice at the plasma membrane, the nascent particle must
undergo a membrane fission event to be released from the cell surface. This release step is
mediated by the cellular ESCRT machinery (Box 1), which is hijacked by Gag. During or shortly
after budding off of the particle from the cell surface, the viral protease cleaves the Gag
polyprotein precursor to trigger HIV-1 maturation.

Virus maturation. When expressed alone, Gag is competent to drive the assembly and release
of non-infectious, immature VLPs. Particle infectivity requires the proteolytic activity of the
viral protease, which is expressed and brought into virions as part of the GagPol precursor.
Concomitant with virus release, the viral protease cleaves a number of sites in both the Gag and
GagPol polyproteins to trigger virus maturation. The HIV-1 protease is an aspartyl protease that
functions as a dimer, in which the active site is located in a cleft at the dimer interface. The
efficiency with which the viral protease cleaves each of its target sites varies considerably,
giving rise to a highly ordered, stepwise processing cascade. Mutations that either increase or
decrease the efficiency with which the protease cleaves a particular site or sites can be highly
detrimental to maturation and particle infectivity, leading to the formation of aberrant, non-
functional cores.

Protease-mediated Gag and GagPol processing is accompanied by a major change in virion


morphology. In the immature particle, Gag molecules are packed in a radial manner. Following
liberation of the individual Gag domains by the viral protease, the CA protein reassembles to
form the conical capsid core.

The organization of CA in the mature HIV-1 capsid core is well defined. The capsid core
assembles with fullerene-like geometry, such that CA forms predominantly hexameric rings to
generate a lattice that is closed off at both ends by the inclusion of pentamers: seven at the wide
end and five at the narrow end. The formation of a hexameric CA lattice with 12 pentamers is a
widespread feature among retroviruses, and the final shape of the capsid core is determined by
the placement of the pentamers (in this sense, the structure of the retroviral capsid core is
analogous to that of a soccer ball, the outer shell of which is composed of a combination of
hexamers and 12 pentamers). Many studies over the years have contributed to our understanding
of the core structure. For example, a combination of cryo-EM and molecular dynamics
simulation generated an atomic model for the HIV-1 capsid core. The inter-hexamer and intra-
hexamer contacts have been defined; as mentioned above, although both immature Gag and
mature CA assemble into hexameric lattices, the intermolecular interfaces in the two structures
differ considerably. Notably, several studies used artificially crosslinked CA hexamers to
overcome aggregation issues during the process of protein purification. However, this problem
was recently solved by crystallizing unmodified CA at low protein concentrations. The resulting
structure provided a detailed view of the native CA–CA interfaces and revealed that water
molecules play an important part in stabilizing inter-hexamer interactions.

In the next round of infection, the viral capsid core provides a degree of protection for the viral
RNA genome as it undergoes reverse transcription. Details of how rapidly and to what extent the
capsid core disassembles — a process known as uncoating — after infection are currently being
investigated. Sensitivity to several post-entry restriction factors maps to CA, indicating that some
CA protein remains associated with the reverse transcription complex after entry. An emerging
view is that at least a remnant of the hexagonal CA lattice stays intact as the reverse transcription
complex traffics to the nucleus; this lattice serves as the recognition signal for host cell
restriction factors and is also recognized by nuclear pore components that play an active part in
the nuclear import of viral DNA. The observation that both increased and decreased core
stability inhibit HIV-1 infection suggests that uncoating kinetics have been precisely optimized
to promote infection

CONCLUSION.

Virus is a small non-cellular parasite of a cell containing a DNA/RNA enclosed in a protein coat.
Some viruses poses an outer envelope made of lipid. The viral structure is very important in
identification. The viral genome codes for enzyme needed for viral replication but do not become
incorporated in the virion and these are called non-structural proteins. During the process of
Reverse transcription, it is catalysed by reverse transcriptase enzymes, that allows retroviruses,
including the human immunodeficiency virus (HIV), to use RNA as their genetic material.
Without reverse transcriptase, the viral genome couldn't become incorporated into the host cell,
and couldn't reproduce.

REFERENCES.

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2. Collier L, and J Oxford, (2006), Human Virology, Oxford University Press Inc, New York
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Press, New Yok.

3. Mahy B. W. J and H. O. Kangro (1996). Virology Methods Manual. Academics Press.

4. Hull R. (2002). Matthews Plant Virology. Elsevier Academic Press.