Lesson 4 - RUA: Principalrua.ua.es/dspace/bitstream/10045/39961/1/Lesson4AMIC-ARA_RUA.pdf ·...
Transcript of Lesson 4 - RUA: Principalrua.ua.es/dspace/bitstream/10045/39961/1/Lesson4AMIC-ARA_RUA.pdf ·...
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Lesson 4
Molecular Virology
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Genetic elements made of living matter molecules, that are capable of growth
and multiplication only in living cells
DIFFERENCE WITH RESPECT TO OTHER GENETIC ELEMENTS:
“They can exist in an extracellular phase that allows their spread”
The extracellular form of the virus (i.e. virion) is metabolically inactive
1.1. Virus Definition
1. Introduction
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1.2. The viral genome
ssDNA
dsDNA
ssRNA
dsRNA
Genome variation (Phase)
Circular or Linear / A single molecule or Segmented
Size: 3-200kb (Phage G, 670 kb)
Gene compaction (overlapping genes …)
Introduction
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1.3. Virus Classification1. Depending on the host
Prokaryotic viruses: Bacterial viruses = bacteriophages or phages; Archaeal viruses
Eukaryotic viruses: protozoan- , fungi-, plant- , animal-viruses
2. Formal taxonomy:
Taxonomic ranks (taxons): order , family, subfamily, genus and species.
FAMILY: unique virion morphology, genome structure (replication strategies).
e.g. Ortomixoviridae, Hepadnaviridae, Poxviridae
3. Baltimore classification: Type of genome and its method of replicaton
Group I: dsDNA (except Group VII)
Group II: ssDNA
Group III: dsRNA
Group IV: ssRNA , positive-sense
Group V: ssRNA, negative -sense
Group VI: Positive-sense ssRNA viruses that replicate through a DNA intermediate
Group VII: dsDNA viruses that replicate through a ssRNA intermediate
Introduction
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1.4. The replication cycle of viruses
2. Penetration (injection)
3. Synthesis of nucleic acids and proteins
4. Assembly and packaging
5. Release (lysis)
1. Attachment (adsorption)
Latency?
Introduction
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1.5. Attachment or Adsorption
Interaction between proteins on the outside of the virus and cell receptors
Receptors: proteins, carbohydrates, glycoproteins, lipids, lipoproteins or complexes
Carry out normal functions in the cell. e.g., Lambda-MalT
Related viruses may not share receptors
The presence of receptors determine which cells are susceptible:
• Species• Strain (phage typing)• Cell type• Tissue
Examples: M13 / E. coli F+
Influenza virus/ Mucous membrane, red blood cells (Sialic acid)
Measles / Any human cell, except red blood cells (CD46)
Introduction
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2. Prokaryotic Viruses
ssRNA+
dsRNA
ssDNA
dsDNA***
MS2
ØX174
M13
T7
T4
Mu
Lambda
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Expression (Transcriptional regulation is not possible)
Temporal programme based on accessibility to AUG codons (RNA structure):
• The more accessible AUG is that of C (translated along the infection cycle)
• Access to the AUG of P is limited. Translation of C grants access to the AUG of P
• Protein C binds to AUG of P and inhibits its translation
• The AUG of A is accessible only in nascent RNA+ molecules
• The AUG of L is partially accessible only when ribosomes reach the stop of C
2.1. RNA phages
Prokaryotic Viruses
MS2 Coliphage
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2.2. ssDNA Phages (Group II)
ssDNA +: replication must precede transcription
Icosahedral: ØX174Filamentous: M13
Prokaryotic Viruses
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2.3. dsDNA Phages (Group I)
• T-uneven phages: T7
• T-even phages: T4
• Mu phage
Prokaryotic Viruses
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T7 Phage
Strategies to maximize genetic economyStrategies to maximize genetic economyStrategies to maximize genetic economyStrategies to maximize genetic economy
• Gene overlap
• Internal translational reinitiation
• Internal frame-shifts
TEMPORAL EXPRESSION PROFILE:
Injection of the genome / Order of genes
Left end.: Early genes
RM system inhibitor
T7 RNA polymerase
Inh. Cell. RNA pol Inh. Cell Expr
First to penetrate
Use the host RNA polymerase
Middle region: Intermediate genes
Use T7 RNA polymerase
Right end: Late genes
Use T7 RNA polymerase
Genome:
Linear
40kb
Direct terminal repeat of 160 bp
Replication
Bidirectional
One origin (closer to left end)
Prokaryotic Viruses dsDNA Viruses
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T4 Phage
Lytic
Linear genome (169 kb)
Complex capsid
• Head
• Neck (with collar)
• Tail (tube + sheath)
• End plate
• Tail fibers
Prokaryotic Viruses dsDNA Viruses
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Linear Genome: Ends?
TEMPORAL EXPRESSION PROFILE
Sequential modification of the host RNA polymerase specificity:
1. Early genes: RNApol-σ 70
2. Intermediate genes: Modification of RNApol α subunit + phage proteins binding
3. Late genes: RNApol-σ Phage
- Form concatamers through recombination
- Sequence-independent Endonuclease
- Regularly spaced cuts (> gene dotation)
- Repeated ends
- Permuted end sequences
Terminal repeats (3-6 Kb)
ReplicationReplicationReplicationReplication
Prokaryotic Viruses dsDNA Viruses: T4
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The Mu Bacteriophage
Temperate
Linear genome
Replication through transposition
Integration is necessary both for lysis and lysogeny
Lysogeny
C Protein
(repressor)Inhibits Transposase
Non-replicative Transposition
Replicative TranspositionLytic cycle
No repression
Prokaryotic Viruses dsDNA Viruses
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50-150 bp Mu=37 kb
1-2 kb
Packaging
Prokaryotic Viruses dsDNA Viruses: Mu
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3.1. Positive-strand RNA
Picornaviridae Family
Polioviruses
Rhinoviruses
Hepatitis A virus (HAV)
Eukaryotic Viruses
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Picornaviridae
- pico means small
- Naked
- Icosahedral
- ssRNA +
Eukaryotic Viruses Positive strand RNA Viruses
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PoliovirusFam. Picornaviridae
- Capsid: 4 proteins, (VP1- 4) x 60
- Intracellular cycle in the cytoplasm
- Genome:
3’ –terminus poly-A tail (copied during replication)
Absence of 5’ cap (Vpg protein)
AAAAAA
Vpg
7.5 kb
- Polymerase is not present in the virion
- Translation of viral proteins must take place before replication
Eukaryotic Viruses Positive strand RNA Viruses
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1 ORF (6620 nt) 1 Polyprotein (proteolytic activity)
Equal amount of every viral protein(anti-economic regulation)
Degradation of EIF-4B(binding of the ribosome to the methylguanosine cap)
Translation of host proteins is blocked
Replication
Requires priming!!: Vpg - UU
Expression
Eukaryotic Viruses Positive strand RNA Viruses: Poliovirus
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3.2. Negative-strand RNA viruses
- Ortomyxovirus
- Rhabdovirus
- Ebola virus
Eukaryotic Viruses
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Ortomyxovirus Fam. Ortomyxoviridae
Influenza virus
New variants (antigenic shift): Epidemics
mixo = mucus
Nucleocapsid:
N Protein
Transcriptase complex (endonuclease)
Envelope: M Protein
Hemagglutinin
Neuraminidase
Genome: Segmented in 8 RNA fragments
Eukaryotic Viruses Negative strand RNA Viruses
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Transcriptase requires 5’ priming to initiate transcription: “stolen” caps
Poly-A: Polymerase slippage
5’-GEndonuclease
Host’s mRNA
5’-GPrimer
5’-G
Viral RNA
5’-G AAAAAAA
Eukaryotic Viruses Negative strand RNA Viruses: Ortomyxovirus
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3.3. dsRNA: Reoviridae Family
Eukaryotic Viruses
Naked
Double-shell Icosahedral capsid (Transcriptase)
Segmented Genome (10-12 dsRNA)
Antigenic shift
REO: Respiratory Enteric Orphan
Rotavirus: Childhood Diarrhea
Facilitates unwinding (replication)
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ProsThe virus can utilize the cellular transcription machinery
The virus con utilize part or all the replication machinery of the cell
Cons
Most cells in an organisms are in a non-division stage
DNA in eukaryotic cells only replicates during the S-phase
3.4. DNA Viruses
ssDNA Parvovirus
dsDNA Papovaviridae (SV40)
Papillomaviridae
Adenoviridae
Herpesviridae
Poxviridae
Eukaryotic Viruses
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3.4.1. ssDNA
Genome: 4,5- 5 Kb (2 genes)
3’ Terminal hairpin Replication primer
Depends on the replication machinery of the host cell
Infect tumor cells or those infected with other viruses (e.g., Adenovirus)
Eukaryotic Viruses
Parvovirus Parvoviridae
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3.4.2. dsDNA Viruses
Adenovirus
Herpesvirus
Poxvirus
Eukaryotic Viruses
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Adenovirus Adenoviridae
Naked Icosahedral virion
Linear of 36 kb
Inverted terminal repeats(100-1800 pb)
- Replication and assembly in the nucleus
- DNA is associated with histones
TP protein
Adeno : Gland
Genome
Eukaryotic Viruses dsDNA Viruses
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- Virus-encoded replication proteins(DNA polymerase)
- Primer: pTP-C
- Initiates at either end:
No Okazaki fragments
Asynchronously
Replication
ssDNA strand
Cyclization, DBPs
Eukaryotic Viruses dsDNA Viruses: Adenovirus
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Herpesvirus Herpesviridae
Herpes simplex
Varicella-Zoster
Epstein-Barr virus
Multilayer Virion
Envelope with spikes
Amorphous Tegument
Icosahedral Nucleocapsid
Linear Genome of 150 kb
Latent in neurons of the sensory ganglia
Eukaryotic Viruses dsDNA Viruses
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REPLICATION
In the nucleus
Circularizes
Rolling circle replication
Concatamers
ASSEMBLY
In the nucleus
Envelope via budding of the nucleus inner membrane
Release through the endoplasmic reticulum
TRANSCRIPTION
α Genes (immediate early)
β Genes (delayed early)
γ Genes (late)
+-
-+
Eukaryotic Viruses dsDNA Viruses: Herpesvirus
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Poxvirus Poxviridae
- The largest animal viruses (300nm Ø):
Smallpox, Cowpox, Myxomatosis…
- Replication IN THE CYTOPLASM
VIRION
Proteins envelope
Genome:
150-200 kb Direct terminal repeat of 10 kbCovalently closed Replication??
dsDNA Viruses
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3.5. Group VI: Retroviridae
Rous sarcoma Virus (RSV)
Human T-cell leukemia Virus (HTLV)
Avian Myeloblastosis Virus (AMV)
AIDS Virus (HIV)
Genome
2 copies of ssRNA + of 7-10 kb
Direct terminal repeats
Cap and Poly-A
Not translated!!
Envelope
Glycoproteins
Icosahedral Virion
2 copies of the genome (ssRNA +)
NucleocapsidRetrotranscriptase
Integrase
tRNA from the previous host
Eukaryotic Viruses
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ssRNA +
Retrotranscription
dsDNA in cytoplasm
Integration in the genome
Transcription:
ssRNA + (genomes, mRNA)
THE REVERSE TRANSCRIPTASE
4 activities :
- RNA-dependent DNA polymerase
- DNA-dependent DNA polymerase
- RNase H, degrades RNA in DNA-RNA hydrids
- Endonuclease
Eukaryotic Viruses Retrovirus
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LTR LTRgag pol env
Retrovirus
cccDNA
Host DNA
Viral
Integrase
ssRNA +
(mRNA, Genomes)
Eukaryotic Viruses Retrovirus
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GENE ORGANIZATION
Three regions:
gag (capsid proteins + protease)
pol ( Retrotranscriptase and Integrase)
env ( Envelope glycoproteins)
Expression (1 RNA = Genome)
Polyprotein
Eukaryotic Viruses Retrovirus