Lecture 8 - (+)-Sense RNA Viruses Flashcards
Baltimore class of most (+)ssRNA viruses
Class IV
(+)RNA viral families
1) Caliciviridae 2) Picornaviridae 3) Togaviridae 4) Flaviviridae 5) Retroviridae (Baltimore VI, not IV) 6) Coronaviridae
Features of viral (+)ssRNA 1) 2) 3) 4) 5) 6)
1) Possible 5’ m7G cap 2) Possible poly-A tail 3) Sequence editing 4) Have no introns 5) Translationally active 6) Resist degradation
(+)ssRNA viruses with 5’ m7G cap and poly-A tail
Coronaviridae Togaviridae
(+)ssRNA viruses with a 5’ m7G cap
Coronaviridae Togaviridae Flaviviridae
(+)ssRNA viruses with a poly-A tail
Coronaviridae Togaviridae Picronaviridae
(+)ssRNA virus without a 5’ m7G cap
Picornaviridae
(+)ssRNA virus without a poly-A tail
Flaviviridae
Only (+)ssRNA virus that carries a capsid polymerase
Retroviridae (carry reverse transcriptase)
Why is the cytoplasm a hostile place for a virus? 1) 2)
1) dsRNA in the cytoplasm is detected, induces IFN secretion 2) Little machinery for genome replication
Gene in coronaviridae, flaviviridae, togaviridae for methyl cap
Methyl transferase enzyme
Essential protein for (+)ssRNA replication
RNA-dependent RNA polymerase (virus encoded)
ssRNA replication 1) 2) 3) 4)
1) Requires RNA-dependent RNA polymerase 2) Can copy both (+) and (-) ssRNA 3) Complex is partly double-stranded (called a replicative intermediate) 4) Normally, few (-) strands are made, and many (+) strands are replicated from the (-) strands
Viruses that make a single RNA
Picornaviridae Flaviviridae
Viruses that make subgenomic RNA
Togaviridae Caliciviridae
Examples of picronaviridae
Poliovirus Hepatitis A virus Rhinovirus
Examples of flaviviridae
West Nile/Dengue virus Hepatitis C virus
Examples of togaviridae
Rubellavirus Ross River virus Sindbis
Examples of calicivirus
Norovirus
Single mRNA method
Viral (+) genome replicates to a (-) genome, which is replicated to a (+) RNA. This (+) RNA is used for both translation and as a genome
Subgenomic RNA method
Viral genome is replicated into a (-) full genome. (-) genome is replicated to either a full genome or a subgenomic mRNA, which is used for protein translation
Poliovirus characteristics
Small, (+) ssRNA virus with a naked icosahedral capsid
What does the poliovirus genome encode?
A single polyprotein
Structure of poliovirus polyprotein
Sections of polio polyprotein 1) 2) 3)
1) 5’ end (P1) is structural proteins 2) P2 encodes proteins that affect the host (stop secretory system, proteases prevent host translation) 3) P3 encodes replicative genes
What cleaves polio polyprotein?
Viral proteases (2Apro, 3Cpro)
What is attached to the 5’ end of polio RNA?
VPg protein
Poliovirus replication 1) 2) 3) 4)
1) VPg protein removed from genome when genome is inserted into cell 2) Polyprotein translated, P2, P3 proteases, enzymes, VPg move to a cytoplasmic membrane-bound vesicle. 3) VPg acts as a primer for RNA-dependent RNA polymerase (3Dpol) replication of (+) and (-) ssRNA 4) Particles assemble in membrane-bound vesicle, are released when cell is lysed
Poliovirus RNA-dependent RNA polymerase
3Dpol
Major issue for (+)ssRNA viruses
Translation occurs 5’ -> 3’ Replication occurs 3’ -> 5’ along (+) strand (assembles (-)RNA 5’ -> 3’) Polymerase and ribosome will collide
Poliovirus RNA replication 1) 2) 3) 4) 5) 6) 7)
1) At the 5’ end of RNA genome is a clover leaf structure. Host PCBP2 and viral 3CD bind this. 2) Host PABP binds 3’ poly-A tail. PCBP2 binds to PABP, forming a loop of RNA. 3) PCBP2 and PABP interactions lead to 3CD cleavage into 3C and 3D-RNA-dependent RNA polymerase. 4) 3D begins replication of genome, utilising VPg-UUU sequence as a primer. 5) Extension of (-) RNA 6) Host chaperone hnRNPC binds ends of (-)RNA. hnRNPC binding to (-)RNA and PCBP2/PABP binding to (+) lead to partial unwinding of dsRNA 7) (+)RNA synthesis occurs from unwound part.
How does poliovirus prevent collision of replication and translation complexes on genomic RNA? 1) 2) 3)
1) A loop of RNA is formed by host PCBP2 binding to 5’ clover leaf structure and host PABP binding to 3’ poly-A tail 2) This loop prevents the access of ribosomes to (+)RNA. 3) Protein synthesis only occurs when the number of genomes outnumbers the number of PCBP2/PABP.
How does poliovirus stop cellular cap-dependent translation?
Polio 2A protease cleaves cellular elF4-G, which is part of the complex that initiates cap-dependent translation
Effect of polio 2A protease cleaving cellular elF4-G
Prevents cellular ability to initiate translation of mRNAs with a cap. This allows only viral proteins to be translated in a cell
How long does it take poliovirus to shut down host-cell translation?
About 2 hours
How does polioviral mRNA initiate translation?
5’ portion folds into an internal ribosome entry site (IRES). Binds directly to cellular translation factors
Characteristic structures in a late-stage poliovirus-infected cell
Double-membrane bound vesicles. Contain dividing virus
How does poliovirus evade IFN production in response to dsRNA detection?
Viral genome replication occurs in vesicles within the cytoplasm.
Why does poliovirus need to replicate genomes within membrane-bound vesicles?
An intermediate stage of viral genome replication is dsRNA. This is detected by a cell and is a powerful stimulus for IFN release
Differences in how hepatitis C virus and poliovirus initiate translation
HCV - Has an internal ribosome entry site (IRES) on the 5’ end Poliovirus - VPg-like protein and an internal ribosome entry site
Does HCV directly kill hepatocytes?
No. Unlike poliovirus, it doesn’t interfere with host cell translation
Togaviridae encoded proteins
Two polyproteins: P123 and P1234
Virus that encodes P123 and P1234
Togaviridae
P123 and P1234 differential expression
Togaviruses have a slippery stop codon that can be read through in their genomes. If translation terminates with the stop codon, P123 results. If the stop codon is read through, P1234 results.
Togaviridae genome replication 1) 2) 3) 4) 5)
1) P123 and P1234 are translated 2) P1234 polyprotein is cleaved by viral protease nsP2. This forms enzymes needed for viral genome replication 3) A (-)ssRNA copy of the genome is made. 4) Two (+)ssRNA copies of the (-)ssRNA genome are made: a genome-length RNA and a subgenomic RNA 5) Subgenomic RNA encodes structural proteins
How do togaviruses regulate when structural proteins are expressed?
1) The subgenomic promotor region only transcribes from (-)ssRNA, which only appears after P123 has been cleaved into enzymes needed for viral replication. Therefore it is initially ‘hidden’ from the host ribosome
Viral family that produces subgenomic RNAs from 3’ end of genome
Togaviridae
How do Togaviridae regulate when structural genes are translated? 1) 2) 3)
1) Capsid genes are at the 3’ end in Togaviridae 2) Togaviridae can produce subgenomic RNAs from the 3’ end of genome. 3) This means that only when replication has been established can capsid proteins be made (as a lot of (-)RNA is needed
How do togaviridae regulate whether full-length RNA or subgenomic RNA are expressed? 1) 2) 3) 4)
1) Progressive proteolytic cleavage of RNA-replicase changes enzyme preference for which RNA to transcribe
2) First cleavage activates (-)RNA synthesis from (+)RNA template
3) Second cleavage activates full genome (+)RNA synthesis from (-)RNA template
4) Full proteolytic cleavage activates subgenomic (+)mRNA for structural proteins from full-length (-)RNA template
SARS coronavirus features 1) 2) 3) 4)
1) Irregularly-shaped enveloped virion 2) Very large (27-31kb) genome 3) Helical nucleocapsid 4) No virion polymerase
Only known helical nucleocapsid with (+)ssRNA
SARS coronavirus
Structure of a coronavirus
E2 - Spike glycoprotein HA - Haemagglutinin (also called E3) E1 - Membrane glycoprotein (also called M) N - Nucleoprotein Es - Envelope glycoprotein
Spike glycoprotein of SARS
E2
Membrane glycoprotein of SARS
E1
Envelope glycoprotein of SARS
Es
Virus with a ‘nested set’ of mRNAs
SARS
SARS replication 1) 2) 3) 4) 5) 6) 7)
1) Enters cell by fusion 2) RNA-dependent RNA polymerase translated fmo genomic RNA 3) (-)ssRNA replicative intermediate is transcribed in the cytoplasm 4) 5’ leader end of the (+)RNA is transcribed with a 5’ methyl cap, added by viral enzyme 5) RNA polymerase skips to downstream sites to make a ‘nested set’ of non-identical mRNAs 6) Viral particles bud into the Golgi 7) Infectious particles are released from the plasma membrane
Formation of ‘nested sets’ of SARS mRNA 1) 2) 3) 4)
1) Genome-length mRNA has a methyl cap added by viral polymerase 2) Common leader RNA sequence is joined to one of many repeated intergenic sequences (UCUAAAC). 3) This leads to the RNA-dependent RNA polymerase to skip the sequences between the common leader RNA sequence and the intergenic sequence 4) This produces a set of 8 discontinuous subgenomic mRNAs
Sequence of repeated intergenic sequence in SARS genome
UCUAAAC
Different locations of structural genes on Picornaviruses and Togaviruses
Structural genes on 5’ end of Picornaviridae genome, on 3’ end of Togaviridae genome
