-
Nucleosides vs nucleotides
- Nucleosides are the substrate for nucleotide synthesis (adenosine, guanosine, uridine, cytidine).
- nucleoTides are the substrate for RNA synthesis (ATP)
-
direction of RNA synthesis
5' to 3', uses ribonucleotides
-
Polymerases (2)
- RNA is synthesized by RNA polymerases.
- DNA-dependent RNA polymerases: use DNA as a template for RNA synthesis. They are the cellular enzymes responsible for synthesis of mRNA, snRNA, rRNA and tRNA.
- RNA-dependent RNA polymerases (RdRps): use RNA as a template for RNA synthesis and are VIRALLY ENCODED ENZYMES.
-
Organisms that use RNA as only genetic material.
Viruses. That's it.
-
replication strategies for RNA viruses (2)
- RNA-dependent RNA synthesis
- RNA-dependent DNA synthesis (reverse transcription, followed by DNA replication and transcription of new viral genomes by cellular RNA polymerase (retroviruses)
-
+ sense vs - sense (vs dsRNA)
- + sense genome: can become a protein immediately, transcribed by host ribosomes
- - sense genome: has to make a copy to become +sense (virion-associated RdRp), THEN transcribed by host ribosomes
- dsDNA genome: transcription by virion-associated RdRp to make +sense RNA, then transcription by host ribosomes.
-
+sense RNA viruses
- naked capsids or be enveloped
- RNA-dependent RNA polymerase synthesized after virus gains access to infected cell
- Single linear RNA genome
-
- sense and ambisense RNA virus families
- enveloped
- RNA-dependent RNA polymerase is inside virion, associated with nucleocapsid
- wrap RNA genome in ribonucleoprotein to form helical nucleocapsids
-
dsRNA virus families
- ds genome is ALWAYS inside a protein capsid.
- virion-associated RNA-dependent RNA polymerase transcribes dsRNA genome segments within viral particle and mRNA extruded from viral particle.
- all dsRNA have segmented genomes
-
Genome of RNA viruses can be a single piece of RNA or can be segmented
Fact
-
Viral RNA-dependent RNA polymerases catalyze two similar but distinct activities
- Transcription (synthesis of viral mRNA)
- Replication (synthesis of viral genomic RNA)
-
monocistronic
- Eukaryotic cells synthesize only one protein per mRNA
- So they synthesize a single long mRNA that encodes a polyprotein that is cleaved (proteolytic) into individual proteins by viral or host cell proteases.
-
How RNA viruses generate several protein products from genomic RNA
- Eukaryotic cells synthesize only one protein per mRNA
- eukaryotic tranlation initiates from a 7-methylguanosine capped monocistronic mRNA and scan from 5' to 3' till they find an AUG codon
- Need more than one protein, but only have one genomic RNA molecule that isn't even capped.
- So they synthesize a single long mRNA that encodes a polyprotein that is cleaved (proteolytic) into individual proteins by viral or host cell proteases.
- OR
- alternatively splice mRNAs (if they replicate in nucleus they can use cellular mRNA splicing machinery
- OR
- transcriptional tricks
- OR
- translational tricks
-
RNA virus genome sequences are highly polymorphic (why?)
- Viral RdRps have minimal proof-reading, are error-prone (fidelity 3 orders of magnitude less than DNA polymerase. Causes antigenic drift) (Ribavirin is a drug that increases mutation to decrease fitness).
- RNA viral genomes can recombine during replication (template switching).
- segmented RNA genomes can reassort (coinfection by 2 viruses causes a combination genome)
-
molecular swarm, aka quasispecies
- high mutation rate leads to incredibly polymorphic population of viral genomes.
- members are genetically linked, can interact functionally and collectively contribute to population characteristics. Allows rapid adaptation of RNA viruses to selective pressure (= resistance to antivirals, vaccine failures).
- MOVING TARGETS for antiviral/vaccine therapy
-
Innate cell defense against viral infection
- secretion of cytokines called interferons (IFNs). Type I IFNs (alpha and beta) induce upregulation of host genes causing apoptosis or interfering with viral replication.
- triggered by viral RNA produced during replication (ds RNA or 5'-ppp end of RNA, as ppp are removed in cellular)
- Cellular sensors detect PAMPs (transmembrane = TLR, intracellular = RIG and Mda-5 detect RNA)
-
How do viruses avoid IFN response
- sequester or hide structured dsRNA: - sense RNA is covered with ribonucleoprotein
- dsRNA viruses always keep genome inside a viral particle
- + sense RNA viruses replicate in sites that are difficult for cellular PRR
- produce viral proteins that block or counteract the anti-viral activation pathways
|
|
