Lecture 9 - (-)-Sense RNA Viruses Flashcards
Which Baltimore class have (-)RNA genomes, which they transcribe to (+)RNA?
Baltimore V
Which Baltimore class has dsRNA genomes, which they use to transcribe to (+)RNA?
Baltimore III
Examples of Baltimore V
Rhabdoviridae
Filoviridae
Orthomyxoviridae
Paramyxoviridae
Examples of Baltimore III
Reoviridae
To which Baltimore class do Rhabdoviridae and Filoviridae belong to?
Baltimore V
Which Baltimore class does Reoviridae belong to?
Baltimore III
Two broad genome types of Baltimore V viruses
1) Segmented genome
2) Non-segmented genome (unimolecular)
First action of a Baltimore V virus upon entering a host cell
RDRP within capsid used to make mRNA from genome
Example of segmented genome
Orthomyxoviridae
Bunyaviridae
Example of non-segmented genome
Paramyxoviridae
Rhabdoviridae
Basic outline of (-)RNA replication 1) 2) 3) 4)
1) (-)RNA used to make (+)RNA, using capsid RDRP
2) (+)RNA makes protein.
3) Replicative protein make (-)RNA (genomic)
4) Structural protein package (-)RNA genome to make virions
Template genome in Baltimore V viruses
(-)RNA
Influenza polymerase complex
PA, PB1, PB2
Examples of rhabdoviridae
Rabiesvirus
Vesicular stomatitis virus
vesicular stomatits virus
1) Rhabdoviridae
2) Single, (-)RNA unimolecular genome
Transcriptional regulation in unimolecular (-)ssRNA viruses
1)
2)
3)
1) Genes are separated by termination and polyadenylation (UUU…) sequences. Start sequence for the following gene
2) RNA polymerase have a high chance of disengaging from genome at each intergenic region. The chance of RNA polymerase re-engaging reduces the further transcription proceeds through the genome.
3) Therefore genes located at the 3’ end of (-)RNA genome are transcribed and translated at the highest levels, as this becomes the 5’ end of mRNA.
Where are structural genes often located on (-)ssRNA genomes?
On the 3’ end
Where are polymerases often located on (-)ssRNA genomes?
On the 5’ end
U7 sequence
Sequence of 7 U between genes on (-)RNA genomes.
This is transcribed as 7A on mRNA. Often, RNA polymerase will add up to 200 A’s, resulting in a poly-A tail
Function of U7 sequence
Leads to poly-A tail formation on mRNA
Examples of henipavirus
Hendravirus
Nipahvirus
To what genus do hendravirus and nipahvirus belong to?
Henipavirus
How do henipaviruses regulate gene expression? 1) 2) 3) 4)
1) P protein is an essential piece of RNA polymerase
2) C protein and V genes lie within P gene
3) V protein is transcribed when a string of G is read by RNApol, RNApol adds an additional G, shifting the reading frame.
4) C protein is made when a second AUG codon downstream of the AUG to make P is read by RNApol.
Genes occupying the same position on genome of nipahvirus
P, C and V proteins.
Role of the C protein in nipahvirus
Blocks IFNa/b signalling.
Role of V protein
Blocks IFNa/b production
Viral protein that blocks IFNa/b production
V protein (nipahvirus)
Viral protein that blocks IFNa/b signalling
C protein (nipahvirus)
How is the nipahvirus C protein transcribed?
Leaky scanning (RNRP binds second AUG)
How is the nipahvirus V protein transcribed?
mRNA editing. RDRP adds an additional G to a poly-G tract
Measlesvirus nucleoprotein size
60kDa
Measlesvirus nucleoprotein function
Self-assembles into a ribonucleoprotein nucleocapsid, by binding to RNA genome, phosphoprotein and RDRP.
Where on measles genome is the nucleoprotein gene?
3’ end (most transcribed and translated protein)
How is measlesvirus genome transcription modulated between mRNA production and genome-length RNA?
High levels of N (nucleoprotein) binding to intergenic junctions promotes RDRP readthrough and production of full-length (+)RNA genome template
Factor that determines whether mRNA or genome-length (+)RNA genomic template is made from measlesvirus genome?
N (nucleocapsid) protein concentration
Influenza genome structure
1)
2)
3)
1) Eight segments.
2) Each (-)RNA segment is bound to RNA polymerase (PA, PB1, PB2)
3) Each segment is coated in nucleocapsid protein (NP)
Influenza envelope proteins
Haemagglutinin, neuraminidase, M2 ion-channel protein, NEP (or NS2).
Gene arrangement on influenza genome
Each of the eight segments encodes 1 gene, except for segments seven and eight, which both encode two genes (different genes expressed by alternative splicing)
NS1 in influenza
Non-structural protein
Signal that is vital for influenza proteins
Nuclear localisation sequence
Why does influenza need to replicate in the nucleus?
Lacks methyl transferase
Only (-)RNA virus that doesn’t replicate in the cytoplasm
Influenza
Influenzavirus replication 1) 2) 3) 4) 5) 6) 7) 8) 9)
1) Sialic acid bound, RME
2) Eight genome segments released into cytoplasm, translocate to the nucleus
3) Viral RDRP makes capped (+)RNA from genome
4) Translation. mRNAs for envelope glycoproteins and M2 ion channel are translocated to the ER-Golgi compartment
5) All proteins are translated into the cytoplasm except for nucleoprotein and RDRP complex (PA, PB1, PB2)
6) Full-length, uncapped, (+)RNA replicative intermediate segments are made, which are templates for (-)RNA genomes
7) M1 and NS1 move to nucleus. M1 binds new (-)RNA, prevents viral mRNA synthesis. Promotes movement of nucleocapsid-coated genome to cytoplasm
8) HA, NA, M2 translated into Golgi, incorporated into cell membrane
9) Nucleoprotein complexed with RNRP, M1, NEP, bud from cell membrane as new virions
How does influenza place caps on mRNA if it encodes no methyl transferase?
1)
2)
3)
‘Cap snatching’
1) PB1 of RDRP complex binds 5’ terminal sequence of influenza genome (highly-conserved)
2) This activates PB2. When cap of host cell mRNA binds to PB2, influenza (-)RNA cyclises.
3) PB2 binds Cap. Cap is cleaved form cellular RNA by PB1, acts as a primer for viral mRNA synthesis
How does influenza regulate whether mRNA or genomic RNA is produced from genome?
1) Viral nucleoprotein levels increase, NP binds to viral RNA preventing PB2 from being able to cap it.
2) PA mediates viral RNA replication, whereas PB2 mediates viral mRNA synthesis
Ambisense genome
Both genomic and anti-genomic strands encode protein
What are all ambisense viruses?
Segmented, (-)RNA
Genera of ambisense viruses
1) Arenavirus
2) Phlebovirus
3) Tospovirus
4) Tenuivirus
Family of ambisense viruses
Bunyaviridae
Diseases caused by bunyaviruses and arenaviruses
Haemorrhagic fevers
Bunyavirus and arenavirus genomes
Ambisense, (-)RNA, Two or three segments
Example of an arenavirus
Lassavirus
Genes encoded on arenavirus segment
1) (+) sense strand - Z protein
2) (-) sense strand - L protein
Ambisense virus transcription and replication
1)
2)
1) RNA folds into hairpins that act as extremely strong stop signals
2) When there is enough N protein, readthrough of stop codons is allowed, forming full-length RNAs
Viruses with segmented dsRNA genome
Reoviridae
Example of a reovirus
Rotavirus
Number of gene segments of rotavirus
10 genome segments
dsRNA virus replication
1) Reoviridae transcribe and replicate dsRNA genome within a protein core. This prevents cell detecting dsRNA and mounting an IFN response
Primary and secondary transcription of rotavirus
1) Primary - Within core, produces mRNA from genome. This occurs upon entry into host cell.
2) Secondary - Upon assembly of capsid. Forms dsDNA from (+)RNA strand
Family to which henipaviruses belong
Paramyxoviridae
