1. RNA viruses: genome replication and mRNA production BSCI 437 Lecture 12
Mechanisms of viral RNA synthesis
Switch from mRNA to genomic RNA production
General comments
All RNA viral genomes must be efficiently copied to provide
Genomes for assembly into progeny virions
mRNAs for synthesis of viral proteins.
Two essential requirements common to RNA virus infectious cycles:
RNA genome copied end to end without loss of sequence
Production of (cellular) translation-competent mRNAs.

2. General strategies for replication and mRNA synthesis of RNA virus genomes. (See Fig 6.1)
(-) Strand RNA viruses

3. General strategies for replication and mRNA synthesis of RNA virus genomes. (See Fig 6.1)
(-) Strand RNA viruses

4. General strategies for replication and mRNA synthesis of RNA virus genomes. (See Fig 6.1)
(+) Strand RNA viruses

5. General strategies for replication and mRNA synthesis of RNA virus genomes. (See Fig 6.1)
(+) Strand RNA viruses

6. General strategies for replication and mRNA synthesis of RNA virus genomes. (See Fig 6.1)
Ambisense RNA viruses

7. General strategies for replication and mRNA synthesis of RNA virus genomes. (See Fig 6.1)
Double-stranded RNA viruses

8. RNA-dependent RNA polymerase (RDRP)
Unique process, no cellular parallel
Hallmark: resistant to actinomycin D, an inhibitor of DNA-directed RNA synthesis.

9. RNA-dependent RNA polymerase (RDRP)
Universal rules:
RNA synthesis initiates and terminates at specific sites in the template
Catalyzed by virus-encoded polymerases
Viral and sometimes host accessory can be required
(most) can initiate RNA synthesis de novo (no primer requirement)
Some do require a free 3’-OH group for priming
Primer can be protein linked
RNA usually synthesized by template directed, stepwise incorporation of rNTPs
Elongation is in 5’  3’ direction
Examples of non-templated viral RNA synthesis exist.
Viral RNA synthesis is highly efficient.
e.g. Poliovirus RNA copied to 50,000 copies in the course of an 8 hr infection

10. Three dimensional structure of RDRPs
Described as analogous to a Right Hand with
Thumb, Palm & Fingers.
Active site located in the Palm subdomain
(Fig. 6.3)

11. Secondary RNA structures
First order information content is contained in the sequence of an RNA
Second order information content is contained the structure
Ability to form G-U base pairs, as well as more exotic non-Watson-Crick base pairs gives RNA the ability to produce a wide variety of structures.
The wide variety of structural possibilities provides for specificity of interaction with other biomolecules, e.g. viral or host proteins.

12. Secondary RNA structures
A wide variety of RNA structures.
Stem regions
Pseuodknots
Each of these can contain un-paired sections called loops
Hairpin loops
Bulge loops
Interior loops
Multibranched loops

13. Roles of viral accessory proteins
Used to direct RDRP to the correct intracellular site.
Nucleus – e.g. Influenza
Membranes – e.g. polio
Can target RDRP to correct initiation site on RNA template
Helicases unwind RNA secondary structures
Processive: unwind along an mRNA
Distributive: unwind at one particular spot
See Figure 6.8 in text

14. Cellular proteins in viral RNA synthesis
In the context of viral genome condensation, viruses have hijacked host proteins to their service.
Qb: RDRP requires ribosomal protein S1, EF-Tu and EF-Ts for their RNA binding properties.
Poliovirus:
host-encoded poly(rC)-binding protein 2 helps target viral proteins to an RNA secondary structure that is the site of initiation for genome replication (see. Fig. 6.8)
Poly-A binding protein 1 (PABP-1) used in both initiation of replication and translation.
Cytoskeletal proteins: used in replication of many RNA viruses. Specific targeting thought to ensure high local concentrations of replication components.
Tubulin: stimulates replication of measles and Sendai viruses.
Actin: Human parainfluenza virus type 3, Respiratory syncytial virus

15. Initiation Mechanisms
Most initiation occurs de-novo.
Exceptions:
Protein Priming: Poliovirus VPg covalently linked to 5’ end of genome. VPg becomes polyuridylated (polyU). Base pairs with polyA 3’ end of genome. Interaction with RDRP serves to target replicase to primed 3’ end of genome. See Fig. 6.8B
Priming by capped RNA fragments: Influenza steals 7Methyl-Gppp caps (cap snatching) from cellular mRNAs by cleaving cellular mRNAs. Cleavage products used to prime viral mRNA synthesis. See fig. 6.9.

16. The Ribosome/RDRP clash problem
In (+) RNA viruses, RNA is both template for translation and replication.
Translation moves in the 5’ 3’ direction along the (+) strand
Replication moves in the 3’ 5’ direction along the (+) strand
Problem: at some point in the middle they will collide. These viruses must evolve around this.

17. Discrimination between viral and cellular mRNAs
Q: How do virus RDRPs discriminate between self and non-self mRNAs?
A: Through secondary RNA structures. Called cis-acting RNA elements.
Often serve as the switches between translation and replication.

18. Synthesis of polyA tracts
3’ polyA tails are required for translation of (most) mRNAs
polyA is attached to the 3’ ends of cellular mRNAs in the nucleus.
RNA viruses replicate in cytoplasm
 Many RNA Viruses have evolved mechanisms to acquire polyA tracts: e.g.
Encode a 3’ polyA sequence on the (+) strand and/or 5’ polyU on the (-) strand
Reiterative copying (“stuttering”) on short 3’ U-sequences on the (-) strand.

19. Switching from mRNA production to genome RNA synthesis
No switch required when mRNA and gRNA are identical.
However, mRNAs of RNA viruses are not complete copies of the viral RNA. A switching mechanism is required.
Different polymerases for different functions
e.g. alphaviruses sequentially produce 3 RDRPs, each with template specificity. The last one is specific for replication of full length genomic RNA
e.g. Influenza and VSV viruses produce two RNA polymerases, only one of which can produce genomic RNA

20. Switching from mRNA production to genome RNA synthesis
Different templates used for RNA synthesis and genome replication
e.g. in dsRNA viruses replication of gRNA occurs only after packaging RNAs inside of capsids.
All unpackaged viral RNAs are mRNA by default.
(fig. 6.17)