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Molecular Virology - Lecture notes

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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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  • December 18, 2023
  • 40
  • 2023/2024
  • Class notes
  • Richard kormelink
  • All classes
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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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