January 2011

(Example: Picornaviruses)

RNA genome viruses account for a wide variety of the viruses that infect us. As we have seen, almost all of these viruses have genomes in the size range from about 8 to 15 Kb, and thus have about 10 or so genes (much smaller than the genomes of the herpesviruses and poxviruses that we have looked at last week). These viruses must code for novel "RNA replicase" type enzymes to replicate their genome. In addition, because we are not dealing with DNA as a template for transcription, we might expect gene expression to be somewhat different than for DNA viruses. Today we will look at the natural replication cycle of picornaviruses, which have an 8 Kb single stranded, positive sense, RNA genome.

1. How can the 8 Kb RNA molecule that is the genome of picornaviruses (poliovirus and rhinovirus) replicate itself and express its genes once it gets into the cytoplasm of a human cell?

See two figures: Overview of picornavirus replication cycle and Picornavirus genome and expression.

A unique and fascinating characteristic of viruses that have a positive sense ss RNA molecule as their genome is that this molecule can function as an mRNA molecule as soon as it gets into the cytoplasm of the host cell. However, as is generally the case with eukaryotic mRNA, only a single polypeptide gets translated (i.e., there is only one AUG codon at which ribosomes begin the translation process). For the picornaviruses, this translated region spans most (about 7500 nucleotides or so) of the ~8000 nucleotides of the genome. That is, ribosomes start translation at an AUG codon some distance in from the 5' end, and stop when they get to an in-frame translation stop codon, which does not occur until near the 3' end of the viral RNA. So, a very large "polyprotein" gets made.

While being made, this polyprotein cuts itself at specific sites by internal protease action. One of the products of this protease action is a viral RNA polymerase, which can use viral ssRNA as template for making a complementary RNA strand. Repeated rounds of synthesis by this enzyme lead to the accumulation of lots of copies of viral +ssRNA in the cytoplasm. These RNAs can then be translated just as the first one was, and so lots of viral polyprotein starts getting made.

2. How can picornavirus assembly be so exact as to result in exactly 60 copies each of the several proteins that make up the icosahedral capsid?

The initial cleavage products that result from the many copies of polyprotein provide many copies of the "P1" piece. Further cleavages of P1 occur, producing a complex of four proteins that then aggregate together to form the pentamer structure. (See figure of picornavirus assembly.) Twelve pentamers aggregate with each other and with a copy of the RNA genome to result in icosahedral virions with exactly 60 copies of all four proteins, the three surface proteins VP1, VP2, VP3, and the internal protein VP4 (associated with the RNA genome).

3. How are the newly assembled virions released from the cell?

By late in the infectious cycle, the cytoplasm of the cell contains hundreds of new icosahedral virus particles. Viral protein 2A (a protease) cleaves a cellular protein ("p220") that is required for translation of normal-capped (cellular) mRNAs. So, while all this picornavirus expression has been going on, translation of cellular mRNAs has been shutting down. As several hours pass, this lack of cellular protein synthesis contributes to the structural deterioration of the cell.


4. What is an example of recent research on picornavirus replication?

Here is an article by Bostina et al titled "Poliovirus RNA Is Released from the Capsid near a Twofold Symmetry Axis", from January 2011 Journal of Virology.