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Summary- Molecular virology (VIR30306)
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Summary- Molecular virology (VIR30306) This summary includes the practical part and the brightspace videos
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Summary Molecular Virologybrightspace videos and practical
Sometimes, a virus contains a genome with multiple open reading frames (ORFs), which can encode
for multiple proteins. This is called polycistronic mRNA.
ORF 1: encodes for RdRp, a RNA polymerase used for replication.
ORF 2: proteins with specific functions, for example the movement protein.
ORF 3: encodes for capsids to produce a cap that protects the RNA.
The viral genome typically has a cap at the 5’-end and a poly-A-tail at the 3’-end.
Only monocistronic (one protein) mRNAs can be translated. Therefore, viruses have multiple tricks for
translation:
Segmentation: the mRNA consists of small segments. Each
segment has the properties of a specific mRNA (including a
cap and a poly-A-tail) that can encode for different proteins
(first image).
Read-through: the ribosome translates the ORF until it
reaches a stop codon. Some stop codons do not always
terminate transcription by ribosomes, the so-called leaky
stop codons. Occasionally, the ribosomes reads through
and can translate a polypeptide until the next stop (second
image).
Leaky scanning: when mRNA has two ORFs. The first ORF
has a weak initiation translation complex, and translation is
sometimes not started. The ribosome continues scanning
until its finds another start codon
(from the second ORF). This leads
to production of two proteins
(image on the right).
Subgenomic messengers: the first ORF can be translated directly
from the viral genome. Translation stops after the first stop codon,
the other ORFs are not translated. The produced RdRp from ORF1
can bind to the 3’-end of the RNA. Here, it can start transcription of the positive sense RNA
into a negative sense RNA. The polymerase makes new positive sense copies from the
negative sense RNA, serving as mRNAs for production of more RdRp. On the negative sense
copy, the polymerase can also start transcription
of subgenomic promotors. Subgenomic
promotors can function in aiding transcription of
, ORF2 and ORF3. These mRNAs are called subgenomic mRNAs, which can be translated into
proteins.
Polyprotein processing: the viral genome contains one ORF, which is translated into one large
polyprotein. A virally encoded protease can cleave this polyprotein into its functional
proteins. Thus, one of the proteins encoded by the
virus, must be a protease.
Frameshift: the first ORF can be translated directly from
the viral genome until the first stop codon. Certain
nucleotide sequences can make the ribosome skip one
nucleotide. Now, it will read a completely different
series of triplets. The first triplets can now be a start
codon, leading to translation of the second ORF.
Influenza virus:
Everything begins when the virus enters the airways, where they specifically attach to the surface of
the epithelial cells. The viral protein HA facilitates binding to the receptors, thereby contributing to
cell entry and viral fusion.
Soluble, cell-bound proteases cleave the HA protein in two parts: HA1 and HA2. The virus is brought
inside the cell using endocytosis. When the pH drops in the endosome, HA1 opens up and allows HA2
to form a triple alpha-helix structure. This structure extends towards the endosomal membrane.
Once the binding is performed correctly, the whole HA protein complex can fold back, allowing the
fusion of the viral genome and its release into the cytosol.
In the cell nucleus, the transcription of the 8 viral strands begins. Fully human monoclonal IgG1
antibodies are capable of neutralizing the virus. The antibodies specifically bind to HA. The antibodies
remain bound to the HA when the pH drops in the endosomes. The antibodies now block the
conformational change of HA1 and thus prevents viral fusion.
Some antibodies can also prevent the initial cleavage of HA.
Retrovirus (HIV):
The retrovirus has an outer envelope, and in the centre, it has two copies of RNA and a reverse
transcriptase. The viral particle can bind to CD4 receptor, the typical receptors for T-helper cells.
Upon binding to the receptor, a conformational change occurs, thereby allowing another receptor,
the CCR5 receptor, to bind to the complex as well.
The envelope protein of the virus start to pull the virus towards the cell, thereby fusing the virus with
the cell.
The virus has a matrix and a capsid protein that are digested once the virus enters the cell. That
releases viral enzymes and the viral RNA. Reverse transcriptase uses host nucleotides to convert the
viral RNA to single stranded DNA. Reverse transcriptase has no proofreading activities so it does make
some errors. The single stranded DNA is further reverse transcribed to double stranded DNA.
Integrase can grab the double stranded DNA and carries it through a nuclear pore inside the nucleus.
Integrase makes a nick in the host DNA, allowing the viral DNA to be inserted into the host DNA.
RNA polymerase can make mRNA, which can be translated to encode for different viral proteins. In
the ER, the envelope protein is transported to the cell surface. Other needed proteins for the virus
are also transported to the cell surface. A protease can cut the polyprotein chain at the cell surface to
form the mature viral particle. This particle can infect other cells.
Lentivirus (HIV): they contain a positive stranded ssRNA. Gag, pol and env are the major genes. The
gag gene encodes for the protective core and matrix proteins for viral assembly and infection. The pol
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