Mobil Genetic Elements -- Viruses and Plasmids

ID #1426

I'm confused by the notes I wrote down on which of the "flavors" of RNA viruses undergo the alternating rounds of genome replication. I know that the minus sense strands must so that they canbe translated, but what about the plus strands? What is their complimentary strand (which would read minus) used for? I also confused myself on viral protease, is it part of the polypeptide chain coded for by the viral DNA now in the host cell's nucleus, or is it made somewhere else?

Here are a couple things to keep in mind when thinking about viral reproductive cycles. First, the type of genome a virus brings in is what it has to package on its way out. Second, replicated nucleic acid molecules are complementary, not identical. And third, some steps in a viral cycle cannot be carried out by host cell machinery and need to be provided by the virus in one way or another.

Now let's get specific. The designation (+) sense and (-) sense are arbitrary designations, and indicate if an RNA molecule can be translated (+) or is the complement of something that can be translated. Keeping all of these things in mind, let's focus on (+) sense RNA viruses. They bring in (+) sense RNA, and that's what they have to leave with. But in order to go from one copy of the genome to 1,000 copies of the genome, a lot of replication has to happen, right? Now, if a (+) sense molecule is the complement of a (-) sense molecule, what is the product of nucleic acid synthesis if you use a (+) sense RNA as template? A (-) sense molecule! Is this what you want to package? No, but there's no other way around it -- you simply can't go from (+) sense to (+) sense in one step, or the virus would be doing that already. Instead, you have to make multiple copies of (-) sense RNA, each of which can now be used as template to make lots and lots of copies of what you really want -- (+) sense RNA. In the meantime, any of those (+) sense molecules can (and will) be used as "message" by ribosomes for the production of viral proteins. So this virus is meeting all its "needs" in as few steps as possible.

The situation for the (-) sense RNA viruses is analogous but reversed. They bring in (-) sense RNA, which not only cannot be translated but cannot be turned into (+) sense RNA in one step. Again, the virus needs an "intermediate" molecule which can act as template for replication of what it really needs and at the same time be translated into viral proteins. As streamlined as it can be!

Regarding the HIV protease, it is a piece of the "polyprotein" translated from the HIV mRNA that has the ability to first cut itself out of the polyprotein and then cleave the rest of the polyprotein into unique HIV proteins. Some of this cutting is being done even as the capsid is being assembled, which is why you can find protease inside the viral capsid on the next round of infection.

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