Flashcards in Virology 2 ( Dr. Balfe): Your cells under new management Deck (29):
Explain the Cheshire Cat escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection.
- coccolithophore has carbonate shells which fix CO2. A single bloom fixes 10% in the UK
- Viruses control CO2 fixation in the ocean.
- Emiliania huxleyi carries a virus... in response to this infection it becomes a haploid to escape the virus. It does not have a carbonate shell in this form.
Do viruses contain ribosomes????
- they do not contain ribosomes because they do not undergo metabolism
Host cell receptors define what with respect to viruses?
- tissue tropism and species tropism
What are the majority of viruses classified as?
- RNA viruses aka Groups three, four, five and six.
3= dsRNA Viruses
4= + Sense RNA Viruses
5= - sense RNA viruses
6= RNA Reverse Transcriptase Viruses
How many viral particles do we breath in every day? What do they mostly comprise of?
- approx > 10,000
- Plant viruses
Explain the difference between antisense and sense strands.
- DNA is normally comprised of two strands an antisense strand and a sense strand. In dsDNA only one strand codes for the RNA that will be translated into protein - the antisense strand is the one that codes for the protein. The strand that does not code for the protein is called the sense strand. Another way of defining antisense DNA is that it is the strand of DNA that carries the information necessary to make proteins by binding to a corresponding messenger RNA. The antisense strand can also be called the noncoding strand.
Viruses that have a single stranded genome can be classified as what two groups?
- Positive strand Virus aka plus strand virus
- Negative strand virus aka minus strand virus
Explain positive strand Viruses.
- these viruses contain single stranded plus strand DNA genomes and transcription of it would yield a message of the minus sense. Therefore, before mRNA can be produced from Class 2 viruses, a complementary DNA strand must first be made to form a double stranded DNA intermediate. This process is called replicative form. The double stranded DNA intermediate is used for transcription and as the source of new genome copies - the plus strand becoming the genome while the minus is discarded.
What different kinds of strands can Negative-Strand RNA Virus genomes have?
-Simple : single piece of RNA that makes ONE protein
- Multipartite, simple
-Multipartite, simple, ambisense OR Multipartite, complex, ambisense
With Negative Strand RNA virus genomes can a naked one make a virus?
- it needs RNA poly to make a positive strand,
Explain some features of positive strand RNA viruses.
- naked RNA CAN form viruses
- can have a conventional cap and tail or one or the other or neither
- genomes are easily broken
- they have a beginning and end
-end= poly a tail
- they make two sorts of proteins ( those that go into the virus and those that dont ie non structural and structural proteins. RNA genomes are extremely small.
What genes are commonly present in RNA Virus genomes? How many genes = typical number?
- RNA polymerase
- Trimeric envelope
- Glycoprotein subunits
-usually manage with X
What does myxo mean in myxoviruses?
- mucus aka these are the cold viruses
Myxoviruses all encode what?
L> a glycoprotein found on the surface of the influenza viruses. It is responsible for binding the virus to cells with sialic acid on the membranes, such as cells in the upper respiratory tract or erythrocytes. It is also responsible for the fusion of the viral envelope with the endosome membrane, after the pH has been reduced. The name "hemagglutinin" comes from the protein's ability to cause red blood cells (erythrocytes) to clump together ("agglutinate") in vitro.
Why were the myxoviruses split by the Baltimore classification?
- some had a single stranded antisense viral genome
- others were multipartite genetic organization with structural complexity. Ex: Influenza virus genome has multiple messages and multiple parts
Explain the myxovirus Influenza.
- it's virus genome is comprised of seven (Influenza C) or eight (Influenza A and B) segments. Each is a single stranded anti sense RNA. All eight segments ahve common nucleotide sequences at their 5' and 3' ends (terminii) and all are necessary for replication of the genome. These segments of genomes can all be swapped around like chromosomes.
- RNA polymerase (three sub units)
- Trimeric envelope glycoprotein
What are the consequences of segmented Virus Genomes ("Viral Sex") ?
- segmented genomes make it possible for the reassortment of genetic information.
- reassortment is a powerful means of achieving rapid generation of genetic diversity, this could be another possible reason for its evolution.
- segmentation of the genome also has implications for the partition and the way in which it is expressed.
- This is how new strains develop and yield massive changes in the virus. Particularly with RNA viruses which are very unstable because they have no proof reading therefore meaning they mutate spontaneously and slowly change over time.
- ex of viral sex can be seen with the combination of bird and human influenxa in pigs.
Explain basic RNA replication.
- Input RNA (-)
- primary transcription occurs yielding mRNA which is translated forming viral proteins and replication occurs.
- replication forms a replicative intermediate (+) which is double stranded RNA and is normally never seen. This triggers an innate immune response leading to the synthesis of IFN (interferon Response)
- the replicative intermediate (+) undergoes secondary transcription and translation yielding a copy of the input RNA (-)
Explain the typical lifecycle of group IV viruses with the running example of HCV.
-HCV has a quadtriple receptor and binds to the membrane of the cell leading to receptor mediated endocytosis.
- virus endosome membrane fusion
- uncoating occurs
- transcription and polyprotein processing
- membrane associated RNA replication
- virus morphogenesis in intracellular vesicles
- virus transport Glycoprotein maturation
-vesicle fusion at the plasma membrane leading to the release of virions.
**90% of RNA viruses treat the nucleus as un needed. They are in the cytoplasm instead.
- RNA viruses love MEMBRANES. Vesicles, endoplasmic R..allows them to contain virus parts...assemble some and associate with the ER
Explain dsRNA virus replication.
- the capsid never fully releases the genome..replicationtakes place in a partially disassembled shell.
- dsRNA viruses have very stable capsids
- Virus enters cytoplasm
- transcription and translation
-virus specific proteins
What are the routes of viral entry?
- plasma membrane
*see text for more info if necessary
Explain retroviruses in terms of replication.
- think Polys
- think lifecycle
- it is very simple with respect to other viruses
- can be RNA dependent RNA poly = RdPp RNA poly
- or RNA dep DNA poly -> RdDp Reverse Transcriptase ****
-The retroviral life cycle begins in the nucleus of an infected cell. At this stage of the life cycle the retroviral genome is a DNA element integrated into and covalently attached to the DNA of the host cell.The genome of the virus is of approximately 8-12 kilobases of DNA (depending upon the retroviral species). Full-length genomic mRNA is made initiating at the beginning ofthe R (repeat) at the 5' LTR (Long Terminal Repeat).The free particle can infect new cells by binding to a cell surface receptor. The specificity of the virus-cell interaction is determined largely by the envelope protein(s) of the retrovirus. Infection leads to injection of the virus nucleoprotein core (consisting mostly of gag-derived proteins, full-length genomic RNA, and the reverse transcriptase protein).
Once inside the cell, the nucleoprotein complex accesses intracellular DNA nucleotide triphosphate pools, whereupon the reverse transcriptase protein initiates creation of a double-stranded DNA copy of the genome of the virus in preparation for integration into the host cell chromosome. Upon completion of reverse transcription, the viral enzyme Integrase searches the DNA for an appropriate "home", whereupon the integrase clips the host DNA and sews the double-stranded DNA into the host DNA. The virus is now prepared to initiate a new round of replication.
Briefly describe the take home message about RNA viruses.
- physical organization of genome = simple vs complex
- genetic organization of RNA transcription = simple vs complex
- common viral replication strategies (devious tricks)
- unique advantages of being RNA based
- unique problems of an RNA genome
- effects of segmented and non segmented genomes and their role in viral evolution
- cause acute resolving infection (ex paramyxoviruses, rotavirus)
- cause chronic infection ( HCV, HIV)
Explain Vaccinia virus plaque formation.
- Vaccinia A33 and A36 proteins are expressed soon after infection and induce actin tail formation
- cells shoot them away via these tails
- stops the cells from taking in more viruses therefore making them spread
- this is why the infection spreads four times to fast. (laws of mass action)
All viruses have to control their hosts. This disruption of the host can range from severe (Polio) to undetectable (HSV). Explain Virally Encoded Host Cell Shutoff (VEHCS) using the classic example of Polio.
- shut off mostly due to cleavage of the 220kD cap binding complex (CBC) which binds the m7G cap structure at the 5' end of all eukaryotic mRNAs and initiates translation. In polio this cleavage of CBC is carried out by Virus Protein 2A
- The 5' UTR of the polio mRNA contains an internal Ribosome Entry site or landing pad which allows virus RNAs to be translated WITHOUT CBC.
- this process is called Virally encoded host cell shut off. All viral infections lead to some sort of virus modulation in the host cell machinery.
Give a timeline of polio infection.
1-2h: Sharp decrease in cell synthesis, migration of chromatin (change in homogenous appearance of nucleus - No cap - no mRNA..no host protein ) CLEAVAGE OF BC BY VP2A
2-5h: start of viral protein synthesis (No cap no prob, Polio mRNA doesn't need it). Vaculoation of cytoplasm, beginning close to nucleus and spreading outwards.
3-4h: Permeabilization of plasma membrane
4-6h: virus assembly in cytoplasm (Crystals sometimes visible)
6-10h: Cell lysis; release of poliovirus particles.
Explain the molecular biology behind VEHCS.
- VP2A ?
- eIF4G ?
- IRES ?
- 3 methods of inactivation?
- VP2A protease that cuts it
- virus directly binds to ribosome for translation therefore making as many proteins therefore shutting off host = virus host shut off.
- eIF4G, a component of the eIF4F cap binding complex, acts as the bridge between the m^7G cap structure and the 40S ribosome subunit.
- IRES = internal ribosome entry site.
1. Cleavage of eIF4G prevents activation via eIF4E
2. Dephosphorylated eIF4E does not bind to eIF4G binds to
3. Dephosphorylated eIF4Ebp binds to and inactivates eIF4E
Explain HSV infection and why it is the perfect game of hide' n' seek.
- it leads to skin lesions and spread to new hosts. BUT a successful immune response to infection eliminates the virus from the skin
- HSV evades the IR by becoming quiescent
- In LATENT infection the HSV genome resides in the nucleus of the host cell and produces NO proteins, just controlling siRNAs derived from latency associated transcripts (LATs)
- Immune recognition REQUIRES protein, latent HSV doesn't make any.
- Herpes shuts down completely. It sends out microRNA which tinker with normal cell machinery to stop the virus from being destroyed.
- The LATs of HSV produce a spectrum of miRNAs which act to control the host cell even though the virus produces no protein. A long list of agents are recognized by the host immune system but nothing on that list is present in latent HSV infection.