DD 02-24-14 08-10am Virus Structure and Function - Kulesza Flashcards
What is a virus?
submicroscopic, obligate intracellular (molecular) parasites that are not themselves alive
How do viruses “grow/replicate”?
In appropriate host cell, genome is replicated & directs the synthesis of components that will be assembled to form progeny viruses; Particles are produced from self-assembly of newly-synthesized components w/in the host cell.
If viruses are not alive, what are they?
Some view them as “chemicals”
3 Strategies Viruses Employ for Survival
- House their DNA or RNA genomes in small proteinaceous particles (capsids).
- Genome contains all info needed to initiate & complete an infectious cycle.
- Establish relationship in a population of hosts that ranges from benign to lethal.
Viruses carry out their 3 basic strategies for survival using a diversity of solution, including variations in…
- Particle architecture.
- Size, nature, topology of genomes.
- Protein coding strategies.
- Cell / tissue / host tropism (i.e. specificty of virus for host).
- Pathogenesis.
Methods for studying viruses
- Electron microscopy,
- Cell culture,
- Animal models,
- Serology,
- Sequence analysis,
- other molecular techniques
2 Virus Classification Systems (name/basic defn.)
- The Classifcal System (viruses grouped according to shared physical properties).
- Baltimore System (based on central dogma, DNA to RNA to protein; categorized by how viruses produce mRNA to code their genomes).
Classical Classification System of Viruses: Shared Physical Properties use to classify:
- Nature of genetic material in the virion (DNA or RNA).
- Symmetry of capsid (helical or icosahedral).
- Naked or Enveloped.
- Dimension of virion & its capsid.
Baltimore system of Virus Classficiation: Reasoning behind
All viruses are parasites of host mRNA translation machinery and therefore, must produce mRNA to decode their genomes; thus, the Baltimore system categorizes viruses based on how they produce mRNA.
Viral Genomes: basics
Consist of either DNA or RNA; have incredible diversity of structure & composition
Viral genome: Plus (+) strands
mRNA containing translatable open reading frame.
“Ribosome ready” = able to be translated into protein.
ALSO the DNA of equivalent polarity to the mRNA.
Viral genome: Minus (-) strands
Complementary sequence to mRNA
DNA from which mRNA is copied.
Two key principles of viral genomes:
- Genomes serve as the template for synthesis of progeny genome; therefore, there is a small, finite number of nucleic acid copying strategies.
- The function of viral genomes once inside the cell is to make mRNA; .
ALL VIRUSES ARE PARACITES OF HOST CELLS mRNA TRANSLATION SYSTEM
Thus, viral genomes must provide mechanisms for the synthesis of mRNA.
Using the two key principles of viral genomes, viral genome configurations can be placed in SEVEN CLASSES:
- dsDNA
- gapped circular dsDNA
- ssDNA
- dsRNA
- ss(+)RNA
- ss(-)RNA
- ss(+)RAN with DNA intermediate
Rearranging the 7 classes of viral genome configuration to match the Baltimore system of viral classification
Group dsDNA genomes with gapped circular dsDNA genomes
Viral Biology of Self-assembly
They are metastable structures subject to conformational changes to promote delivery of genome to appropriate host cell.
This viral assembly / disassembly are targets for several anti-viral drugs.
Overview of Functions of Virion Proteins
- Protection of genome.
- Delivery of genome.
- Mediate interaction with host.
Virion Proteins’ Functions: Protection of genome
- Asssembly of stable protective protein shell.
- Specific recognition & packaging of nucleic acid genome.
- In some cases, interact with host cell membranes to form the envelope.
Virion Proteins’ Functions: Delivery of Genome
- Specific binding to external receptors of host cells.
- Transmission of specific signals that induce uncoating of genome.
- Induce fusion w/host cell membranes.
- Interact with internal components of host cells to direct transport of genome to form the envelope.
Virion Proteins’ Functions: Mediate interactiosn w/ the host
- Interact w/ host components to ensure efficient viral replication.
- Interact w/ cellular components to transport to sites of assembly.
- Interact w/host immune system.
Viral particle arrangements / creation
Created by symmetrical arrangement of many identical or highly similar proteins in ways that provide max contact & non-covalent bonding between them.
Capside proteins of different viruses…
have highly conserved structural motifs, alothough protein sequences themselves may not be conserved
Genome delivery occurs because…
Structure is not permanently bonded together (non-covalent) and thus can be taken apart to release genome to initated new infection.
Thus, the functions of viral particles depend on very stable interactions of their components during assembly, egress, & transmission, BUT also ready reversal of these interactions during entry & uncoating in a host cell.
Self-assembly & Symmetrical viral structure
Symmetry solves difficulty of viral self-assembly.
All but the most complex animal viruses display either helical or icosahedral symmetry.
How symmetric architectures is achieved…
Achieved through the organized self assembly of viral proteins:
Each subunit engages in “identical” non-covalent bonding contactes with its neighbors…
This repitition of “identical” interactions among a limited number of proteins results in a regular structure. If “non-identical” bonds form, aggregates or clumps are made. Thus, the symmetry & form of a viral structure depends on the spatial patterns of the interactions.
Helical capsids
Simplest way to arrange multiple identical subunits & used by a large number of viruses infecting all forms of life. Uses rotational symmetry & arranges irregualrly shaped proteins around a circumference of a circle to form a disk.
Icosahedral capsids
Arranges proteins subunits in the form of a hollow, quasi-spherical structure which encloses the genome within. Done in several ways, depending on shape of repeated subunits; but “naturally” occurs by using triangle as the repeating unit (pic in notes)
Icosahedron =
Solid shape consisting of 20 triangular faces with 12 vertices and faces with 2-, 3- and 5- fold axis of symmetry.
Icosahedral symmetry in viral capsids
May not actually be icosahedrons, but have more complex arrangement of facets w/in the triangular faces. (see pic in notes); Smallest is constructed of 60 identical subunites (3 unites per face). Larger volumes accomplished by using more protein subunits.
Viral Envelope: Purpose
Add layer of complexity to virus structure/function
Viral Envelope: Structure
Lipid bilayers acquired during assembly of viral particles, typically with viral glycoproteins embedded in them.
Viral Envelope: Origin
Usually acquired by budding through the membrane of the host cell into some extra-cytoplasmic compartment (either through plasma membrane itself, or through the membrane of the ER or Golgi.
Escape from infected host by Non-enveloped viruses vs. Enveloped viruses
Non-enveloped:
Typically lyse infected cell (kill it).
Enveloped:
Bud through membrane & form envelope as the last step in viral assembly = important in virus’s mechanism of escape from infected host cell; DOES NOT NECESSARILY KILL the host cell.
Viral glycoproteins’ roles in Viral Life Cycle
- Entry / Host range determination.
- Assembly & egress.
- Evasion of vertebrate immune system
Viral glycoprotein structure
Integral membrane proteins, usually with 1 or 2 transmembrane domains.
Oligomeric, non-covalent assemblies.
Viral vs. Bacterial Growth
Viruses DO NOT grow exponentially like bacteria do.
Rather, virus is released as a “burst,” due to the fact that viruses are assembled from preformed components.
One step growth curve
Experiment done in cultured cells where every cell is infection with virus.
Between 0-12 hours after viral absorption, no virus is detectable inside or outside cell (eclipse period).
Latent period is the time between the initiation of the infection and the rlease of new infectious virus particles FROM THE CELL (~16 hrs for Adenovirus type 5, in pic in notes).
Eclipse period
Represents time when virus particles have broken down after penetrating cells, releasing their genomes as a prerequisite for replication.
They are no longer infections at this stage and cannot be detected as plaque forming units (PFUs) in the assay.
Latent period
- Attachment of virus to cell.
- Entry of virus into cells & un-coating of viral genome.
- Viral gene expression.
- Viral genome replication.
- Assembly of new viruses and egress of new virus particles from cell.
Viral Attachement
Involves specific binding of virus-attachement protein w/ a cellular receptor molecule.
Target receptor molecules of viruses:
- Proteins (usually glyco-).
- Carbohydrates (found on glycoproteins or glycolipids); usually less specific that protein receptors b/c the same configuration of carb side chains may occur on many different glycoslated membrane bound molecules.
Viral Entry
Penetration of traget cell by virus normally occurs very soon after attachment step.
This step is generally energy-dependent (unlike attachment)– thus cell must be metabolically active for it to occur.
Mechanisms for Viral Entry
- For both enveloped & non-enveloped viruses, endocytosis of virus into intracellular vesciles (endosomes), from which the virus must ultimately escape; common mechanism.
- For enveloped viruses, fusion of viral envelope w/cellular membrane (plasma
Uncoating of virus
General term for events occuring after viral particle has entered the cell, in which viral capsid is completely or partially removed and viral genome is exposed
What viral genome encodes (at minimum)
proteins required for genome replication, assembly of capsids, & modulation of host cell processes to maximize viral production
DNA viruses (composition, template for transcription)
- Double-stranded, gapped genomes or single stranded genomes.
- Must transcribe mRNA using the (-) strand of the DNA genome as template
Requirements for transcriptions of DNA virus genes
Since it uses the (-) DNA strand as template, gaps must be filled (or genome must be replicated in the case of ssDNA) before genes can be transcribed…
Performed by RNA polymerase II in the nucleus of infected cells
Produces classical mRNAs that are capped & poly-adenylated (by host machinery).
Replication is exclusively nuclear & depends on cellular structures (though some viral enzymes / accesory factors are used as well).
Exception to requirements of transcription of DNA viruses
Poxviruses
= replicated in cytoplasm of infected cells and encodes own RNA polymerase
= replication is largely independent of cellular machinery
RNA viruses (important component)
All contain unique viral enzyme called RNA-dependent RNA polymerase (RdRp)
= not found in host cells
= for both the production of mRNA and the replication of RNA genomes
(+) stranded RNA viruses - translation process, RdRp role
Can be translated directly by ribosomes.
RdRp mediates amplification of mRNA copy number or production of sub-genomic mRNA.
(-) stranded RNA viruses & double-stranded RNA viruses
(+) sense mRNA must be transcribed from genome in order to have gene expression
Animal cell cannot do this.
This genome is not “ribosome-ready”
So viruses must bring the necessary enzyme (RdRp) in with them.
Retroviruses - what are they
(+) stranded RNA viruses with DNA intermediate
Retroviruses - translation process
- Before gene expression, must copy their single-stranded RNA genome into dsDNA; accomplished by reverse transcriptase (enzyme packaged into virus particle)…animal cells DO NOT contain an enzyme that can do this…
- Then, dsDNA copy of the genome integrates into the host cell DNA.
- Then, mRNA is transcribed from the virus genome using host cell-encoded RNA polymerase II.
Site of replication & machinery used for dsDNA viruses
Most: nuclear, using cell’s machiner
Exception: Poxviruses: cytoplasm, using viral replication factors
Site of replication & machinery used for ssDNA viruses
Nuclear
Involves double-stranded intermediate serving as template for synthesis of ssDNA
Replication machinery used for gapped circular stranded DNA viruses
Nuclear (?)
Uses virally encoded reverse transcriptase to copy viral genomes from mRNAs transcribed from template genome into dsDNA, then cellular RNA pol II translates the dsDNA in mRNA.
Viruses with RNA genomes
Transcription & Genome replication are highly integrated.
Genome replicated using anti-genome template.
Both production of this anti-genome & replication of the genome is accomplished by RdRp (see pic in notes)
Icosahedral capsids: Assembly
Packaging of genome into capsid performed in 2 ways:
- Capsid assembles around the viral genome.
- Genome is “fed” preformed capsids.
Helical capsids: Assembly
Viral genome is generally coated w/ nucleocapsid protein during its synthesis.
Effect of Assembly on Host Cells
Often resutls in significant cytopathic effect (CPE) b/c capsid proteins are produced to very high levels in infected cells.
Their abundance results in either cytoplasmic or nuclear inclusions (depending on location of assembly), often detectable by light microscopy.
Size / location of inclusion is often characteristic of particular virus.
Egress
Exit from infected cell.
Different for enveloped vs. non-enveloped cell…
Egress w/enveloped virus
Envelope acquired from a variety of cellular membranes via process called “budding.”
Viruses that bud into plasma membrane are released into extracellular environment directly…
Viruses that bud into membranes of Golgi or ER are secreted from infected cell.
Egress w/non-enveloped virus
“Naked capsids” = often release from infected cell via lysis; so much virus is produced & cell is so compromised, that it just breaks open.
