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Summary

Virology Tutorials Summary

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  • Module
  • Virology (BMB430006)
  • Institution
  • Universiteit Utrecht (UU)

This is a summary I made while following the tutorial of the (electives) Virology course. The main viruses are covered during the tutorials are summarized in this document. Other life sciences master's program can also take this course as an elective. Alongside the tutorials, the lectures are also ...

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Document information

  • January 7, 2024
  • 25
  • 2023/2024
  • Summary

Subjects

  • poliovirus
  • alphavirus
  • influenza virus
  • herpes simplex virus

Written for

  • Universiteit Utrecht (UU)
  • Infection and Immunity
  • Virology (BMB430006)
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Poliovirus
Viral structure
The poliovirus was first discovered in 1909 by Landsteiner & Popper
and named after the disease it caused, poliomyelitis. It is an
animal virus that only infects humans and is classified into 3
serotypes (Type I/II/III) based on an antibody neutralization assay.

The virus has a relatively small size of 30nm. It is a naked (+)
stranded RNA virus with an icosahedral capsid. This capsid has
canyon grooves around the 5-fold symmetry axis where it binds to its
receptors (CD155). The poliovirus capsid is made out of 3 structural
proteins: VP1, VP2, and VP3 which all have a 𝛽-barrel jelly roll structure.
Both VP2 and VP4 make the VP0 protein which gets cleaved during virion
maturation. VP4 is not visible from the outside but is important for
stabilizing the capsid from the inside. The icosahedral capsid is made upon
a pseudo T=3 organization. It is actually a T=1 capsid, but VP1 and VP2 in
the capsid are so similar, they behave within the structure in the same
manner, that it seems to be a T=3.

Inside the capsid, VP4 interacts with myristate (lipids) and VP3 to stabilize
the structure. The internal structure is not​complete until the final​stages
of virus particle​production​. VP0 is cleaved into VP2 and VP4 probably to
destabilize the capsid so it can uncoat for the infectious cycle. The capsid
is a very stable structure since it can auto-assemble. However, if it is too
stable, it cannot dissociate anymore. Thus, some destabling mechanism is
needed.

Infectious cycle
The poliovirus infectious cycle occurs in around 6-8
hours and can produce 10.000 virions/cell.
1. The virion binds to a cellular receptor, CD155
2. enters an endosome (endocytosed)
3. Release of the poliovirus genome occurs from
within early endosomes located close to the
plasma membrane (within 100 to 200 nm).
4. The VPg protein, depicted as a small orange
circle at the 5′ end of the RNA genome, is
removed, and the RNA associates with
ribosomes.

,5. Translation is initiated at an internal site 741 nucleotides from the 5′ end of the viral mRNA, and a
polyprotein precursor is synthesized.
6. The polyprotein is cleaved during and after its synthesis to yield the individual viral proteins. Only
the initial cleavages are shown here.
7. The proteins that participate in viral RNA synthesis are transported to membrane vesicles. RNA
synthesis occurs on the surfaces of these infected-cell-specific vesicles.
8. The (+) strand RNA is transported to these membrane vesicles
9. Copied into double-stranded RNAs.
10. Newly synthesized (−) strands serve as templates for the synthesis of (+) strand genomic RNAs.
11. Some of the newly synthesized (+) strand RNA molecules are translated after the removal of VPg.
12. Structural proteins are formed by partial cleavage of the P1 precursor
13. association with (+) strand RNA molecules that retain VPg to form progeny virus particles.
14. Released from the cell upon lysis.

Replication
Entry
Receptor: CD155 (Pvr)​
Binding of the receptor leads to
rearrangement of capsid into the
expanded form, called particle A
(altered) and the virion gets
endocytosed​. Receptor binding
also causes a conformational
change that removes sphingosine
from the capsid, resulting in
destabilization. This destabilization
allows VP1 to insert into the
endosome membrane and the
internal VP4 to get exposed to
form a pore through which the
release of genome​occurs.

Genome organization




5’ VPg covalently bound to the cloverleaf (first 108 nucleotides), secondary structures at 5’ (IRES) and 3’
(polyA tail) UTRs, internal Cre​. There is only 1 ORF → 1 polyprotein (needs proteolytic processing)​.

, Translation
Upon uncoating, VPg gets cleaved
by TBP2 (unlinking enzyme​) which
allows host ribosomes to bind to
the (+) strand RNA. Cap
independent and IRES dependent
translation occur when 40S binds
and scans for AUG. Translation
leads to the formation of one long
precursor polyprotein which gets
cotranslationally processed by
2Apro and 3Cpro. The 5’ cap
recognition motif in eIF4G is
cleaved by 2A, but the C-terminus
end can still bind to IRES and
recruit other host proteins for
translation.

Polyprotein processing
2A autocleaves P1 (structural proteins) and P2P3. 3CDpro is
a protease. Upon high protein concentration, it gets
cleaved to make 3Cpro and 3Dpol. This will favor replication
over translation as 3Cpro is less efficient than 3CDpro. 2BC
and 3A are needed for pore forming in the release stage.
3B is VPg. 2C uses ATP to remodel the ER and golgi
membrane, forming membranous viral-induced organelles
where they perform replication. 3a infiltrates the lipid and
integrates as a membrane bound protein.

Replication
(-) strand synthesis:
1. Ribonucleoprotein (RNP) complex formation:
poly(rC)­binding protein 2 (PCBP2) and 3CDpro at the
cloverleaf structure of (+) strand RNA.
2. The RNP interacts with poly(A)­binding protein 1
(PAbp1) which is bound to the 3′ poly(A) sequence,
bringing the ends of the genome into close proximity.
3. 3CDpro cleaves membrane­ bound 3AB → VPg and 3A.
(​​VPg doesn't only come from the cleaved 3AB but can
also be recruited from those translated).

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