Lecture notes

Molecular Virology - Lecture notes

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Module
Molecular Virology (VIR30306)

Institution
Wageningen University (WUR)

Book
Fundamentals of Molecular Virology

Lecture 1 - Introduction Lecture 2 - Plant viruses (+mRNA) Lecture 3 - Picornaviruses (Polio) Lecture 4 - negative RNA Bunyaviruses Lecture 5 - negative RNA Influenza viruses Lecture 6 - Retroviruses / HIV Lecture 7 - RT DNA viruses: para-retroviruses Lecture 8 - DNA Baculovirus Lecture 9 -...

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Uploaded on December 18, 2023
Number of pages 40
Written in 2023/2024
Type Lecture notes
Professor(s) Richard kormelink
Contains All classes

protein coat
envelope
positive ssrna
negative ssrna
dsdna virus
plant viruses
segmentation
subgenomic rna
cell entry
replication
translation
transcription
polio
influenza
hiv
bunyaviruses
pararetrovir

Book Title:Fundamentals of Molecular Virology

Author(s):Nicholas H. Acheson, N. H. Acheson

Edition:Unknown
ISBN:9780470900598
Edition:Unknown

Lecture notes
Lecture 2 Poliovirus and HIV

Institution
Wageningen University (WUR)
Education
MSc Biotechnology
Module
Molecular Virology (VIR30306)

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Lecture 1 - Introduction
Virus
= genetic entities (RNA or DNA) protect by protein coat , sometimes also a lipid membrane
which uses the synthesizing system of host witch has pathological effects on the host cell

all organisms have
viruses

Pathogens smaller than virus:
- Viroid = only RNA, circular, disease making
- Prions = disease making proteins, misformed

Composition of a virus
- viral genome (RNA or DNA)
- protein shell, made up from CPs
= coat proteins
- lipid membrane / envelope
- GP = envelope glycoprotein

Baltimore classification
= Classification based on how viruses make
+mRNA from their genomic material.

-ssRNA → viral RNA polymerase needed

Protein coat
Why subunits: coat proteins (CPs)
- saving genetic space on small genome
- increasing genetic stability (smaller gene → lower risk for mutation)
- easy (dis)assembly
- symmetric → minimal energy & less visible for immune system

,Function protein coat
- protection of genetic material
- recognition and penetration of the host cell

Structure
The higher the fold, the more spherical the protein coat will be

T=3 icosahedral capsid protein T=16 icosahedral capsid protein
pentameres = 12 asymmetric units = 5*12 = 60 capsid proteins = 60*T

T=triangulation, the higher the T → bigger particle
because capsid proteins are the same size

Entry of virus into the cell
1. Attachment
2. (internalization in endosomes)
3. Fusion
4. Transport

Classification
➢ molecular architecture
➢ replication strategy
➢ genetic relatedness
➢ host organisms

bacteriophages = viruses that infect bacteria

,Lecture 2 - Plant viruses (+mRNA)
The eukaryotic protein translation system Plant viral ss(+) RNA genome organization

The plant translational machinery only multiple ORFs
translate monocistronic messengers
(mRNAs) = one open reading frame (ORF)

ORF1 replication
(polymerase, helicase, methyl transferase)
ORF2 movement
UTR = untranslated region ORF3 encapsidation (coat proteins)
viral mRNA needs to mimic the eukaryotic mRNA
Strategies to overcome differences in mRNA:
1. Segmentation one ORF per mRNA

2. Subgenomic one ORF mRNA split of from
RNAs the main mRNA

3. Read-through only part of mRNA is
translation transcribed due to weak
start/stop codon

4. Frame shifting ribosome shifts to another
ORF so not all ORF translated

5. Polyprotein transcribed as one protein,
then processed into multiple

Cucumber mosaic virus (CMV) Tobacco mosaic virus (TMV)

2. Subgenomic RNA
1. Segmentation 3. Read-through translation
2. Subgenomic RNA

, Potato virus Y (PVY) Potato leafroll virus (PLRV)

5. Polyprotein

part of polyprotein can be protease → cuts
others (trans) or itself (cis)
2. Subgenomic RNAs
3. Read-through translation
4. Frame shifting
5. Polyprotein

Infection cycle
Virus entrance
Mechanical rupture in the cuticle caused by:
- Piercing → aphid, whitefly, thrips, nematode
- Biting → beetle
- Handling of plants
no receptor-mediated endocytosis like with animal-infecting viruses

Replication & translation
First translate protein needed for
replication
→ co-translational disassembly

Then +ssRNA → -ssRNA → +ssRNA
→ co-replicational disassembly

Translation of
movement/encapsidation proteins

Then assembly of new viruses

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