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VIROLOGY > 3 – Virus Replication > Flashcards

3 – Virus Replication Flashcards

1
Q

What are the 3 fundamental properties in the basic common strategy for viral replication?

A
  1. All genomes are packed in particles that mediate host-to-host transmission
  2. Viral genomes contain necessary information to initiate and complete an infectious cycle within a susceptible, permissive cell
  3. Viral propagation is ensured by viruses establishing themselves in a host population
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2
Q

What is the necessary info viral genomes have to complete an infectious cycle within a susceptible, permissive cell?

A
  • Virion attachment and entry
  • Decoding genetic information
  • Genome replication
  • Assembly and release of particles that contain the genome
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3
Q

What does replication require of a target cell?

A
  • Susceptible: virus can enter
  • Permissive: virus replication is supported
    o Complementarity of virus-host protein-protein interactions
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4
Q

What initiates the virus from entering cells?

A
  • Chance encounter of viral particle and a SUSCEPTIBLE cell
    o More particles increases probability of infection
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5
Q

What must happen for the virus to enter cells?

A
  • Bind to cell: usually a specific interaction between particle and cell surface receptor
    o Virus-receptor interactions may be highly selective (or not)
  • Cross the plasma membrane (some cases also the nuclear membrane)
  • Disassemble to release genetic information
    o Targeted to the correct cellular compartment
  • *virus may use different entry mechanism to enter different target cells
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6
Q

What do viruses need to bind to initiate entry? Both for enveloped and non-enveloped viruses

A
  • Enveloped: glycoproteins
  • Non-enveloped: capsid proteins
  • *expression of host cell receptors determine HOST RANGE and TISSUE TROPISM for infection
    o Receptor modifications can be another determinant of tissue tropism
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7
Q

Receptor modification can be another determinant of tissue trophism, ex. influenza and sialic acid residues

A
  • Human IAV strains preferentially bind sialic acids attached to galactose via an alpha 2,6, linkage
  • Avian IAV preferentially bind to alpha 2,3 linked sialic acid
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8
Q

Viruses and host cell receptors

A
  • May use more than one host cell receptor
  • Cellular receptor may be used by more than one virus
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9
Q

What happens when a virus binds to host cell receptor?

A
  • Can initiate intracellular signaling pathways
    o Beneficial to viral entry and propagation/pathogenesis=induce uptake through endocytic pathways
    o Detrimental to viral propagation/pathogenesis=triggering antiviral responses
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10
Q

What is entry receptor identification a combination of?

A
  • Molecular cloning
  • Use of monoclonal antibodies
  • DNA-mediated transformation
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11
Q

What happens if expression of the receptor on a cell results in binding, but not infection?

A
  • A coreceptor is required
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12
Q

What does knocking out the receptor in cells that normally express it do?

A
  • *resistant to infection
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13
Q

What happens if permissive cells that don’t express the receptor are made to express it?

A
  • Receptor expressing cells can then be infected
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14
Q

What do antibodies that bind to receptor do?

A
  • Fusion at plasma membrane
  • Attachment and uncoating at the plasma membrane
  • Endocytosis
  • Macropinocytosis
  • Antibody-dependent enhancement of entry (ADE)
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15
Q

Fusion at the plasma membrane (fusion of viral envelope and plasma membrane)

A
  • Achieves uncoating and delivery of genome to the functional cellular compartment in a single step
  • Releases capsid/core into the cytoplasm
    o Transported and dismantled to release viral genome to the functional cellular compartment
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16
Q

Attachment and uncoating at the plasma membrane

A
  • Process of absorption, uncoating, and entry of Parvoviridae genomic DNA into nucleus is POORLY understood
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17
Q

Endocytosis

A
  • Many use host cell endocytic pathway to enter
  • Multiple mechanisms
  • Viruses may enter a cell via more than one mechanism
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18
Q

Adenoviridae endocytosis to enter cell

A
  • partial disassembly in the endosome, followed by release
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19
Q

Picornaviridae endocytosis to enter cell

A
  • release of genome occurs from early endosome
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20
Q

Reviridae endocytosis to enter cell

A
  • in endosomes and lysosomes acid-dependent proteolysis alters the virion to a form that can penetrate the endosomal membrane to release the core into cytoplasm
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21
Q

Rhabdoviridae endocytosis to enter cell

A
  • fusion of viral membrane with endosome membrane releases nucleocapsid into the cytoplasm (functional compartment)
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22
Q

Orthomyxoviridae endocytosis to enter cell

A
  • acidification of endosome results in fusion of viral membrane with endosome membrane releases nucleocapsid into cytoplasm
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23
Q

Macropinocytosis (ex. Filoviridae)

A
  • enters via micropinocytosis and is trafficked to a late endosome
  • fusion of viral and endosomal membrane releases nucleocapsid into the cytoplasm
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24
Q

Antibody-dependent enhancement of entry (ADE)

A
  • non-neutralizing antibodies coat the virus and facilitate uptake by cellular Fc recptors
  • not fully understood: can be Fc or complement-mediated
  • *vaccines can induce ADE
  • Ex. Dengue fever virus, West Nile Virus
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25
Q

Some need cell transport mechanisms to deliver capsid to functional cellular compartment before uncoating

A
  • Utilize cellular endocytic pathway and cytoskeleton
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26
Q

Parvovirus and hepadnavirus nuclear entry mechanism

A
  • Capsids are small enough to enter through nuclear pore
    o Bind to pore complex and disrupt the nuclear envelope and nuclear lamina for entry
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27
Q

Adenovirus nuclear entry mechanism

A
  • Nuclear pore docking results in capsid dismantling to allow vDNA transport into the nucleus
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28
Q

Herpes simplex virus nuclear entry mechanism

A
  • Nuclear pore docking results in EXTRUSION of vDNA through a capsid portal into nucleus
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29
Q

Influenza virus nuclear entry mechanism

A
  • Genomic segments are small enough to transport through the nuclear pore
30
Q

Some retroviruses nuclear entry mechanism

A
  • Enter nucleus after the nuclear envelope breaks down during cell division
    o Restricts infection to cells that undergo mitosis
31
Q

Viral genome production is a combined effort between viral proteins and cellular synthetic machinery

A
  • Cell provides nucleotides, energy, many necessary enzymes and other proteins
  • Virus provides template and specialized proteins
32
Q

Some genomes require modification or other viral nucleic acids for replication

A
  • DNA polymerase have proofreading capacity
  • DNA viruses are replicated with high fidelity
33
Q

What must ALL viruses make for synthesis of viral proteins by cellular translation machinery?

A
  • Make mRNAs
34
Q

What is RNA synthesis from RNA templates unique to?

A
  • RNA viruses
    o No cellular machinery to do this job
    o Virus must bring it or have it made
35
Q

What do all RNA viruses encode?

A
  • RNA-dependent RNA polymerase (RdRp)
    o May or may not require a primer to initiate synthesis
    *use cellular protines
    *RNA genomes in virion may be naked OR bound by proteins
36
Q

What can nuclear replicating DNA viruses and retroviruses use?

A
  • Cellular DNA-dependent RNA polymerase (DdRp, usually RNAPII)
  • Ex. poxviruses: DNA viruses that replicate in cytoplasm, must bring their owen DNA-dependant RNA polymerase
37
Q

What is reverse transcriptases (RTs)?

A
  • Synthesize DNA from RNA and DNA
  • Lack proofreading activity (ERROR PRONE)
  • Slow
  • Require a primer: cannot initiate DNA synthesis de novo
  • Ex. retroviruses, hepadnaviruses
38
Q

Hepadnaviral example (reverse transcriptases)

A
  • Replication of genomic DNA has a RNA intermediate
  • Newly synthesized pregenomic mRNA serves as template for reverse transcriptases
  • ALL DNA is produced by reverse transcriptases
    o DNA episome is NOT replicated by host machinery
39
Q

What is integrase?

A
  • Recombinase that inserts retroviral DNA into host genome (Provirus)
  • Ex. retroviruses are the ONLY animal viruses that encode an integrase
  • *critical step in retroviral replication cycle that ENSURES stable association of proviral DNA with host genome
    o Final step is repaired through a host-cell mediate process
40
Q

dsDNA (I): Viral genome may be linear or circular. What accomplishes mRNA synthesis or genome replication?

A
  • Host or viral DNA-dependent RNA or DNA polymerases
41
Q

ssDNA(II)

A
  • dsDNA must first be made
    o RNA synthesis requires a ds template
  • ssDNA genomes are produced by cellular DNA polymerases
42
Q

ds gapped DNA (VII)

A
  • *circular genome is partially dsDNA
  • gapped genome is produced from an RNA template
  • gaps must first be filled in by host cell enzymes
  • *host RNAPII can only transcribe dsDNA
43
Q

dsRNA (III)

A
  • (+) strand of dsRNA not suitable template for polymerase
    o Cannot be translated as part of duplex
  • (-) RNA stand is copied into mRNA by an RdRp
  • Synthesized (+)RNAs can be translated or encapsidated to template dsRNA synthesis
44
Q

(+)ssRNA (IV)

A
  • (+)RNA genome can be translated by host ribosomes
  • Genome replication requires synthesis of (-)RNA template
  • Full-length copies of (+) RNA can be mRNA or packaged as genomes
45
Q

(-)ssRNA (V)

A
  • (-) RNA genome must be copied into (+) mRNA for translation
  • (-) RNA genome is also the template for full (+)RNA strands, which are copied to produce more (-)ssRNA genomes
    o Some (-)ssRNA genomes are segmented (ex. Orthomyxoviridae)
    o Some (-)ssRNA have ambisences (+ and –) genomes
  • Replication of RNA genome is required for additional (+) information to be translated
46
Q

(+)ssRNA (VI)

A
  • (+)ssRNA genome are first converted to a dsDNA intermediate
    o dsDNA integrates into host genome
  • mRNA and genomic (+) RNA synthesis is mediated by cellular enzymes
47
Q

What are some strategies to pack the most coding information into the smallest genome possible?

A
  • Subgenomic mRNA (ex. alphavirus)
  • mRNA splicing (adenovirus)
  • RNA editing
  • Nested transcription units
  • Info on both strands (dsDNA)
48
Q

Viral proteins that stimulate RNAPII transcription can establish regulatory gene expression circuits (2)

A
  1. Positive autoregulatory loop
  2. Transcriptional cascade
49
Q

Positive autoregulatory loop (viral mRNA expression)

A
  • Viral protein stimulates transcription rate without altering viral transcription complement
50
Q

Transcriptional cascade (viral mRNA expression)

A
  • Viral transcription units activated in an ordered sequence to ensure different protein classes are made at different times of the infectious cycle (DNA virus characteristic)
  • Early phase and late phase
  • *ensures coordinated production for particle assembly
51
Q

Transcriptional cascade: early phase

A
  • Express viral proteins necessary for efficient viral gene expression, DNA synthesis, other regulatory functions
52
Q

Transcriptional cascade: late phase

A
  • Express viral proteins necessary for virion formation (structural proteins) usually after genome replication
53
Q

What is the differences in gene expression between viruses with DNA genomes and RNA genomes?

A
  • DNA genomes: ordered gene expression
  • RNA genomes: continual gene expression of ALL GENES
54
Q

How might viruses interfere with cellular processes to selectively promote viral mRNA synthesis and translation?

A
  • Inhibit cellular transcription or mRNA processing/export
  • Promote degradation of or ‘deface’ cellular mRNAs
  • Interfere with translation regulatory proteins
55
Q

What are all viral mRNAs translated by?

A
  • Cellular translation machinery (cytoplasmic)
56
Q

What can expand the coding capacity of the viral genome?

A
  • Variety of unusual translation mechanisms
  • *support synthesis of multiple proteins from a single RNA genome
57
Q

What is monocistronic?

A
  • Eukaryotic mRNA
    o One protein from one mRNA
58
Q

What is polycistronic?

A
  • Bacterial and archaeal mRNA
    o Multiple proteins from one mRNA
  • *some viruses encode bicistronic mRNAs
59
Q

What are internal ribosome binding sites (IRES)?

A
  • RNA structures that support internal ribosomal binding for translation initiation
60
Q

What are some other translation strategies to increase genome coding capacity?

A
  • Ribosomal frameshifting
  • Termination suppression
  • Reinitiation
  • Leaky scanning
  • *polyprotein processing
61
Q

Polyprotein processing

A
  • Some viruses synthesize polyprotein precursors that are proteolytically processed to form the functional viral proteins
  • *nearly the entire (+) RNA is translated into a large polyprotein
    o viral proteases are active in nascent polypeptide and release by self-cleavage
    o AA residues flanking the cleavage sites control cleavage efficiency: so NOT ALL cleavage sites are processed
62
Q

What do cellular chaperones ensure?

A
  • Proper folding of membrane proteins in ER
  • *processed proteins delivered to virion assembly site via cellular secretory pathway
63
Q

What are some post translational modifications?

A
  • Proteolysis
  • Glycosylation
  • Fatty acylation
  • Phosphorylation
  • SUMOylation
64
Q

Assembly of components needs to occur and can occur in different compartments. Example for DNA viruses

A
  • Nuclear capsid requires nuclear import of structural proteins
65
Q

Viral particle assembly

A
  • Requires cellular transport systems
  • Info is contained within primary sequences of viral structure proteins
    o May be improved by cellular or viral chaperones or scaffolding proteins
  • *viral genomes often contain specific packing signals
66
Q

Envelopes of many viruses are acquired from internal membranes of infected cell (rather than PM)

A
  • Viral glycoproteins sort to internal cell membranes for viruses that BUD into the compartments OR are wrapped by cellular membranes during assembly
67
Q

Components may be sorted to specialized surfaces in polarized cells (ex. epithelial cells, neurons)

A
  • Enveloped viruses may be released from APICAL or BASAL surfaces of epithelial cells
    o Apical: shed into respiratory or genital secretions; intestinal contents
    o Basal: systemic spread via bloodstream or lymphatics
  • *implications for the efficacy of the immune response
68
Q

How can viral particles be released?

A
  • Secretory pathway (ex. hepatitis B virus, herpes simplex virus)
  • Budding at PM (enveloped viruses)
  • Lysing the cell
  • Cell to cell spread
  • *some undergo FINAL processing to a mature, infectious form during or after RELEASE
69
Q

Cell to cell spread of viral particles

A
  • Avoids exposure to host antiviral defense mechanisms
  • *implications for the efficacy of the immune response
70
Q

What ultimately determines the outcome of infection?

A
  • Interplay of virus-host protein-protein interactions
71
Q

What does successful synthesis of viral components and infectious particle assembly require?

A
  • Takeover of the host cells metabolic and biosynthetic processes
  • Signal transduction pathways
  • Trafficking systems

VIROLOGY (12 decks)

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