VIR30306-Molecular Virology complete summary with all lectures included
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Course
VIR30306
Institution
Wageningen University (WUR)
This summary has 50 pages with explanatory figures taken from the lecture slides. This summary contains all the relevant information from all the lectures and covers all chapters. This course is mandatory for all master students following medical biotechnology specialization. With this summary Igo...
They are genetic entities of RNA or DNA protected by a protein coat and sometimes a lipid
membrane, which upon infection of a suitable host control the synthesising system of the cell in such
a way that new viruses are produced.
Often coinciding with visible pathological effects on the cell and the organism: causal agents of many
infectious diseases.
3 main properties:
- Infectivity→ property to infect the cell to multiply and to leave the cell.
- Extracellular state
- Obligatory intracellular parasites
Viruses are also ideal for bio-molecular studies and biotechnology applications.
They are nanoparticles; therefore we require electron microscopy to see them.
+ Process:
1. Enter the cell → distinct ways to do so.
2. Multiplies by taking over the host mechanism
3. Spreads and leaved the cell
Genome size can vary a lot depending on the virus size, can be from 2000nt, which is around 2 genes,
or giant viruses of up to 1200000nt which are around 900 genes.
There are 2 entities smaller than a virus:
- Viroids→ stunted plant viruses→ only RNA (250-300nt).
- Prions→ misfolded proteins that can bind to functional proteins rendering them inactive→
Creutzfeldt-Jacob, BSE.
+ Virus composition:
Viruses that contain a lipid membrane or an
“envelope” are usually viruses related to
human/animal infecting viruses.
➔ They have glycoproteins for receptor-
mediated endocytosis.
Composition of viruses → Viral genome, proteins
(usually a coat, shell protein) and some have a lipid
membrane or envelope.
1
,+ Viral structure:
Protein shell (or coat) is built up by smaller subunits→ the coat proteins (CPs). Why?
- They save genetic space on the small genome.
- They increase genetic stability (smaller gene: lower risk for mutation).
- Easy (dis)assembly.
- For constructing a symmetric virus particle (virion).
Symmetry in viruses in crucial→ they use it as escaping tools of the host immune system by
minimising the number of “neutralising epitopes”.
Forms of viruses:
a) Rod-shaped viruses → helical symmetry
By arrangement of identical, asymmetric components around the circumference of a circle
would yield a symmetric structure.
Helical NOT circular→ As an helical structure there are no package limitations as particle
length is determined by the size of the genome. Protein subunits arrange around it.
b) Isometric viruses → architecture based on icosaeder
Five platonic bodies: tetrahedron, octahedron, cube, dodecahedron, and icosahedron. The
last one is the preferred morphology of a virus since it is the most symmetric of the bodies.
The icosahedron allows for the lowest-energy configuration of particles interacting
isotropically on the surface of the sphere.
Isotropic → not comparable. In an isotropic manner, so as to exhibit the same properties or
behaviour in all directions.
Example: adenovirus
On the surface of an icosahedron→ 60
copies of and (asymmetric) protein can be
placed.
All isometric viruses have an icosahedral
symmetry but can be smaller or bigger
depending on the genome size.
This is calculated by the triangulation
number→ the larger the particle the larger
the triangulation number.
c) Complex viruses → combination of both and even more.
Example is the bacteriophage.
+ Infectious cycle:
1st: entry process → can vary between viruses, but usually the viral proteins create a fusion pore,
that allows the inside viral content into the host cell.
- It is a multistep process that involved attachment, fusion and transport.
- For each virus is different and the attachment can be due to different receptors.
nd
2 : Viral replication→ usually they first create more viral mRNA. After that they guide the host
machinery to produce the viral genome and finally the viral capsid proteins for assembly.
3rd: Spread out of the cell→ different machinery such as taking host cell membrane, bursting out the
cell etc.
2
,+ Classification of viruses:
1. Molecular architecture:
- RNA or DNA
- Single stranded or double stranded
- Linear7circular
- Capsid symmetry/envelope
2. Replication strategy→ Baltimore classification
The viral diversity is huge, for that reason there needs to be some sort of classification.
This classification is based that all viruses have to produce an mRNA→ therefore depending on
the viral genome, one or more steps need to be taken to create a mRNA that can be translated
by the host mechanism.
Six types:
I. Double stranded DNA→ positive strans can
be read into an mRNA directly.
II. Positive ssDNA → doubled and synthesised
into mRNA.
III. Retroviruses ( dsRNA)→ directly
translated.
IV. Positive ssRNA→ doubled and translated.
V. Negative RNA → directly translated.
VI. Retrovirsues (positive ssRNA)→
retrotranscribed to negative DNA, doubled and
translated.
+ What is the difference between a positive strand and a negative strand of RNA?
The mRNA is a positive RNA which is then translated to protein.
- Positive ssRNA can be directly translated and therefore they are directly infectious.
- Negative ssRNA cannot be directly transcribed, they first need to create a positive RNA
strand. They are not infectious. They usually contain a
polymerase for this.
3. Genetic relatedness→ phylogeny (evolutionary,
development and diversification of a species or group or
organism or a particular feature of an organism).
4. Host organism→ transmission.
+ Taxonomy of viruses:
There are orders, families, subfamilies, genus and species.
Eaxmple in vertebrates:
3
, 1. PLANT VIRUSES: POSITIVE SENSE (+) RNA viruses
Most of the plant viruses are ss (+) RNA→ 77%
Positive single stranded RNA can be directly translated upon infection into the host cell.
The RNA virus infects the cytoplasm where the translation machinery is located.
The DNA viruses infect the nucleus because there is where the transcription machinery is.
Genome organization→ mimic the host mRNAs.
+ Plant host RNA:
5´cap → inverted and methylated GTP → protects from
degradation and gives orientation for the ribosome to
bind.
3´poly A tail→ signal to stop translation.
Untranslated regions are at the 3´and at the 5´end.
Monocistronic →1 ORF→ 1 protein
+ Plant viral genome:
5´end → methylated G cap or VPg (viral protein genome-linked)
3´end → poly A tail or tRNA-like folded RNA structure.
They are polycistronic→ more than 1 ORF and therefore more than one single protein translated.
They require different proteins that usually the host cannot provide, such as RdRP (RNA dependent
RNA polymerase), which is present in the nucleus and not the cytoplasm.
1.1. STRATEGIES FOR VIRAL RNA TRANSLATION/PROTEIN PRODUCTION
The plant virus mRNA is similar to the host plant virus; however, they are polycistronic and yet
they manage to hijack the plant translation mechanism. How?
a) Segmentation of the genome → minimize downstream ORFs
The mRNA is divided in different segments → each segment has a 5´cap or VPg and a 3´poly
A tail of tRNA like structure.
Each segment codes for a protein.
Example: cucumber mosaic virus (CMV).
b) Subgenomic RNAs → temporal regulation of gene expression
Genome RNA machinery recognises inner starting sited → creates a shorter version of the
transcript which codes for a distinct protein.
Usually the subgenomic RNAs are produced later in the infection, but depends on what the
virus requires at that time.
Example: CMV too.
c) Read-through translations → leaky termination or initiation
1 long mRNA which multiple ORF.
Readthrough the stop codon → very weak stop codon can be overread and continue with
the translation of the coming ORF.
Different RNA subunits can bind together to make another protein too.
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