Submitted by not_my_usual_name t3_11pzyw4 in askscience
If one bit of the RNA the virus injects, when read by the cell's machinery and assembled into a protein, builds one bit of the copy virus' RNA, then the copies can't have both a full copy of the RNA and a capsule and other proteins. Is there some compression involved? Is there a command the virus uses so it can say "build me a capsule, these proteins, and then copy this entire strand of RNA?"
And open reading frames, overlapping genes, and a bunch of other neat tricks.
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For coronaviruses the genome is translated into a big polyprotein which is cleaved in a dozen of proteins by a protease it includes. That dozen of proteins somehow self assemble into a replication complex which also makes the (lipid) ER membrane bubble. Into such a bubble the viral polymerase of the replication complex replicates the genome many times and also makes many subgenomic mRNA coding for the structural proteins. Eventually the bubble bursts and frees the many copies of the genome and the many subgenomic mRNA, those are translated and flood the environment with viral structural proteins. Together with the copied genomes all this mess self assemble into new virions. Both the bubbling and the natural cellular transport of membrane anchored proteins help the new virions to egress the cell.
Hope this helps your understanding of the standard strategy for virus replication.
This is interesting. My understanding was always that the viral RNA is seen as RNA coming from the cell's DNA, and the cell's protein assembling machinery would assemble a virus according to the virus' RNA. You're saying that the virus' RNA actually has the cell's machinery assemble a virus factory "replication complex"?
Presumably in the replication complex, there's some molecule producing viral RNA. Does it do that by looking at and copying the original strand of RNA (or copies)? If not, then was the RNA production machine built "knowing" how to make the viral RNA? I'd think that involves some compression, which is what I'm most curious about.
All the translation (making of proteins) is done by the cell's ribosomes (this for almost every viruses) from mRNA strands as the cells do everydays to make proteins.
But the replication and transcription (making copies of the full length RNA genome and some mRNA copied from parts of it) is achieved by a viral polymerase, a RdRp.
This is for RNA viruses. Many DNA viruses do something along the same lines, but some do not and make their genome enter the cell nucleus to exploit either its DNA replication machinery or its DNA->RNA transcription machinery, or both.
Retroviruses are some kind of hybrid between the two strategies.
>If one bit of the RNA the virus injects, when read by the cell's machinery and assembled into a protein, builds one bit of the copy virus' RNA, then the copies can't have both a full copy of the RNA and a capsule and other proteins.
Why not? Are you assuming the RNA is consumed when it's read? It's not. Or are you thinking it can only be read in one way? There are two different kinds of systems for reading genetic information and making something based on the sequence. The ribosome reads three RNA bases at a time, dictating a protein sequence. Polymerases read one base at a time by matching up base pairs before insertion.
What I mean is that if each base in the injected RNA specifies exactly one base of the produced RNA, then there aren't any bases left in the injected RNA to specify how to build anything but an identical strand of RNA. It seems like there must be something more efficient going on, and I'm interested in what it is from an information science perspective.
If there's a sequence of AUG in an RNA, then an RNA-dependent RNA polymerase can copy that to UAC in a newly synthesized RNA, because those bases "fit" in base pairs. Then the UAC in that RNA can be copied into AUG in a new RNA that's identical to the original one.
A ribosome can read the exact same AUG sequence and insert a methionine into a protein.
One method is essentially just straight copying while staying in the same language, while the other is translating to a different language. That's why the process of making proteins is called translation.
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Viral RNA will have multiple genes that code for different things. I’m the case of coronaviruses, the RNA will have a gene that codes for a polymerase that makes copies of the whole rna genome and have genes that code for the proteins necessary to make a virus particle.
In the case of retroviruses, they don’t have a code to copy their own RNA that leaves the infecting virus particle but instead they convert their RNA genomes into DNA and integrate into the cellular DNA at which time they use the cell’s own machinery to make RNA.
EdSmith77 t1_jc24psa wrote
Viral RNA typically will code for multiple different proteins in one strand of RNA. So for example the HIV viral RNA is thousands of bases, and codes for many proteins (protease, reverse transcriptase, capsid, etc.).