Lecture 9 - (-)-Sense RNA Viruses

Question 1

Which Baltimore class have (-)RNA genomes, which they transcribe to (+)RNA?

Answer 1

Baltimore V

Question 2

Which Baltimore class has dsRNA genomes, which they use to transcribe to (+)RNA?

Answer 2

Baltimore III

Question 3

Examples of Baltimore V

Answer 3

Rhabdoviridae
Filoviridae
Orthomyxoviridae
Paramyxoviridae

Question 4

Examples of Baltimore III

Answer 4

Reoviridae

Question 5

To which Baltimore class do Rhabdoviridae and Filoviridae belong to?

Answer 5

Baltimore V

Question 6

Which Baltimore class does Reoviridae belong to?

Answer 6

Baltimore III

Question 7

Two broad genome types of Baltimore V viruses

Answer 7

1) Segmented genome

2) Non-segmented genome (unimolecular)

Question 8

First action of a Baltimore V virus upon entering a host cell

Answer 8

RDRP within capsid used to make mRNA from genome

Question 9

Example of segmented genome

Answer 9

Orthomyxoviridae

Bunyaviridae

Question 10

Example of non-segmented genome

Answer 10

Paramyxoviridae

Rhabdoviridae

Question 11

Basic outline of (-)RNA replication
1)
2)
3)
4)

Answer 11

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

Question 12

Template genome in Baltimore V viruses

Answer 12

(-)RNA

Question 13

Influenza polymerase complex

Answer 13

PA, PB1, PB2

Question 14

Examples of rhabdoviridae

Answer 14

Rabiesvirus

Vesicular stomatitis virus

Question 15

vesicular stomatits virus

Answer 15

1) Rhabdoviridae

2) Single, (-)RNA unimolecular genome

Question 16

Transcriptional regulation in unimolecular (-)ssRNA viruses
1)
2)
3)

Answer 16

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.

Question 17

Where are structural genes often located on (-)ssRNA genomes?

Answer 17

On the 3’ end

Question 18

Where are polymerases often located on (-)ssRNA genomes?

Answer 18

On the 5’ end

Question 19

U7 sequence

Answer 19

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

Question 20

Function of U7 sequence

Answer 20

Leads to poly-A tail formation on mRNA

Question 21

Examples of henipavirus

Answer 21

Hendravirus

Nipahvirus

Question 22

To what genus do hendravirus and nipahvirus belong to?

Answer 22

Henipavirus

Question 23

How do henipaviruses regulate gene expression?
1)
2)
3)
4)

Answer 23

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.

Question 24

Genes occupying the same position on genome of nipahvirus

Answer 24

P, C and V proteins.

Question 25

Role of the C protein in nipahvirus

Answer 25

Blocks IFNa/b signalling.

Question 26

Role of V protein

Answer 26

Blocks IFNa/b production

Question 27

Viral protein that blocks IFNa/b production

Answer 27

V protein (nipahvirus)

Question 28

Viral protein that blocks IFNa/b signalling

Answer 28

C protein (nipahvirus)

Question 29

How is the nipahvirus C protein transcribed?

Answer 29

Leaky scanning (RNRP binds second AUG)

Question 30

How is the nipahvirus V protein transcribed?

Answer 30

mRNA editing. RDRP adds an additional G to a poly-G tract

Question 31

Measlesvirus nucleoprotein size

Answer 31

60kDa

Question 32

Measlesvirus nucleoprotein function

Answer 32

Self-assembles into a ribonucleoprotein nucleocapsid, by binding to RNA genome, phosphoprotein and RDRP.

Question 33

Where on measles genome is the nucleoprotein gene?

Answer 33

3' end (most transcribed and translated protein)

Question 34

How is measlesvirus genome transcription modulated between mRNA production and genome-length RNA?

Answer 34

High levels of N (nucleoprotein) binding to intergenic junctions promotes RDRP readthrough and production of full-length (+)RNA genome template

Question 35

Factor that determines whether mRNA or genome-length (+)RNA genomic template is made from measlesvirus genome?

Answer 35

N (nucleocapsid) protein concentration

Question 36

Influenza genome structure 1) 2) 3)

Answer 36

1) Eight segments. 2) Each (-)RNA segment is bound to RNA polymerase (PA, PB1, PB2) 3) Each segment is coated in nucleocapsid protein (NP)

Question 37

Influenza envelope proteins

Answer 37

Haemagglutinin, neuraminidase, M2 ion-channel protein, NEP (or NS2).

Question 38

Gene arrangement on influenza genome

Answer 38

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)

Question 39

NS1 in influenza

Answer 39

Non-structural protein

Question 40

Signal that is vital for influenza proteins

Answer 40

Nuclear localisation sequence

Question 41

Why does influenza need to replicate in the nucleus?

Answer 41

Lacks methyl transferase

Question 42

Only (-)RNA virus that doesn't replicate in the cytoplasm

Answer 42

Influenza

Question 43

``` Influenzavirus replication 1) 2) 3) 4) 5) 6) 7) 8) 9) ```

Answer 43

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

Question 44

How does influenza place caps on mRNA if it encodes no methyl transferase? 1) 2) 3)

Answer 44

'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

Question 45

How does influenza regulate whether mRNA or genomic RNA is produced from genome?

Answer 45

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

Question 46

Ambisense genome

Answer 46

Both genomic and anti-genomic strands encode protein

Question 47

What are all ambisense viruses?

Answer 47

Segmented, (-)RNA

Question 48

Genera of ambisense viruses

Answer 48

1) Arenavirus 2) Phlebovirus 3) Tospovirus 4) Tenuivirus

Question 49

Family of ambisense viruses

Answer 49

Bunyaviridae

Question 50

Diseases caused by bunyaviruses and arenaviruses

Answer 50

Haemorrhagic fevers

Question 51

Bunyavirus and arenavirus genomes

Answer 51

Ambisense, (-)RNA, Two or three segments

Question 52

Example of an arenavirus

Answer 52

Lassavirus

Question 53

Genes encoded on arenavirus segment

Answer 53

1) (+) sense strand - Z protein | 2) (-) sense strand - L protein

Question 54

Ambisense virus transcription and replication 1) 2)

Answer 54

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

Question 55

Viruses with segmented dsRNA genome

Answer 55

Reoviridae

Question 56

Example of a reovirus

Answer 56

Rotavirus

Question 57

Number of gene segments of rotavirus

Answer 57

10 genome segments

Question 58

dsRNA virus replication

Answer 58

1) Reoviridae transcribe and replicate dsRNA genome within a protein core. This prevents cell detecting dsRNA and mounting an IFN response

Question 59

Primary and secondary transcription of rotavirus

Answer 59

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

Question 60

Family to which henipaviruses belong

Answer 60

Paramyxoviridae