Novel biochemistry in Bovine immunodeficiency virus

Many roads lead to Rome-- there is no one 'right' way to solve an evolutionary hurdle. Viruses encounter the same evolutionary 'problems', but have evolved lots and lots and lots of different solutions to the exact same problems. Random chance of mutations + the bumbling blindness of natural selection ('good enough' is selected, not 'BEST!') means all that bumbling mess leads to different 'solutions'. Some might work better than others, but they all work, and thats good enough.

Its easy to comprehend an RNA virus doing something differently than a very distantly related DNA virus. But differences exist between closely related viruses as well. We all know no-new-genes-no-new-functions Michael Behe and his Creationist BFFs hate the evolutionary capacity of new-genes-new-functions HIV-1. They have to hate its cousin Bovine immunodeficiency virus too:

The bovine immunodeficiency virus Rev protein: identification of novel nuclear import pathway and nuclear export signal among retroviral Rev/Rev-like proteins

There are lots of different ways to get a protein. Retroviruses operate like a sheet cake-- it makes one bit mRNA that gets cuts up into lots of little mRNAs as it leaves the nucleus, which go one to be translated into all the proteins the retrovirus needs.

... But then how to you get a retroviral genome into the babby viruses? The retroviral genome is a big uncut piece of mRNA. If it always gets cut up when it leaves the nucleus, how can you ever get that big uncut RNA genome into new viruses?

Lentiviruses have an answer to this dilemma-- "Regulator of Virion Expression", Rev.

Rev escorts the mRNA out of the nucleus, so it can be chopped up in different ways to get different retroviral proteins, or, prevent the RNA from being cut entirely so full genomes can be packaged into babby viruses.

And of course, its not just about Rev getting out of the nucleus with its RNA companion.  It must also be able to get itself into the nucleus.  Proteins like Rev are made in the cytoplasm on ribosomes-- it needs to perform a few tricks to get itself into the nucleus to pick up its RNA buddy.

So Rev does two things-- gets into the nucleus, gets out of the nucleus with RNA.  Gets into the nucleus, gets out of the nucleus with RNA.  Over and over.

You would think that Rev from HIV and Rev from BIV would look and behave in the same manner.  Theyre the same protein from the same family of retrovirus (lentivirus) that accomplish the same function.

Youd be thinking wrong!

1-- BIV Rev has a bipartite nuclear localization signal (NLS).  HIV Rev has a monopartite NLS (translation, the genes look different).

2-- BIV Rev gets into the nucleus via the classical importin alpha/beta nuclear import pathway.  It requires a carrier and energy to get in.  HIV Rev just needs an importin (beta, 5, 7, 9) or transportin.  BIV cannot get in the same ways HIV Rev gets in (these researchers tried).

3-- There are two kinds of nuclear export signals (NES), HIV Rev-class, and PKI-class.  BIV Rev NES is not an HIV Rev-type.  It is PKI-type!

What does this all mean?

In conclusion, we characterized the mechanisms of the nuclear import and export pathways of BIV Rev. The nuclear import of BIV Rev differs from that found in HIV-1 Rev. Although BIV Rev is exported by CRM1, its NES belongs to the PKI-class. In addition to the previously described novel types NLS/NoLS, these mechanisms make of the BIV Rev an unique protein within the retrovirus/lentivirus field.

Sure, HIV and BIV are both 'retroviruses'.  They are both 'lentiviruses'.  They both have a 'Rev' protein.  The Rev protein 'does the same thing' in both-- carrying RNA out of the nucleus, running back in, carrying RNA out of the nucleus, running back in.

But that function is performed by Rev proteins that look and behave in totally different manners.

Novel genes.

Novel functions.

Poor Creationists.

Even the cows are against them.

More like this

So Rev does two things– gets into the nucleus, gets out of the nucleus with RNA. Gets into the nucleus, gets out of the nucleus with RNA. Over and over.

Am I the only one who found this bit kinda sexy?

I am?

Oh well.

By Optimus Primate (not verified) on 14 Jun 2012 #permalink

hey abbie, sorry for my bad english.

if a news function need somthing like 20-30 new amino acid it may be possible. but what about a protein that need minimum 2 binding site?(like the enzyme aminoacyl-trna synthetase).

a minimal binding site need somthing like 50aa(from article in nature 2001)/ so we will need to change 100aa at once.

its very unlikley in space of 20^100 possible combination.

Here are the first couple of answers I can think of to your question (I imagine there are more possibilities as well):
The easiest one (for me, for the virus), is that the virus just stole a cellular sequence - that is, the viral DNA /or/ RNA spontaneously recombined with cellular sequences that just happened to work, and work a little better, for this particular function, and it was retained due to natural selection.
Alternately, small modifications can occur over generations; as new viruses infect cells, they mess up a little by changing, adding and removing sequences each time. This might not drastically affect the function of the protein, and thus, the modifications are kept, and compounded upon. As long as the virus is fit enough to keep replicating (matching or out-competing other sequences and dodging the host's defenses) and infecting, these modifications can accumulate over generations until they generate a considerably different protein than the original one. At some point, should this collection of changes confer a new, useful function, or improve upon a previous function, they become much more strongly selected for, and are kept for following generations of virus. Although I'm not sure where specifically the 20^100 possible combinations came from, if you think of all the BIV genomes and all their predecessors that have ever been generated through replication, and all the errors (of varying kinds - inserts, deletions, nucleotide substitutions) that could occur in each genome, even this slow, complicated approach becomes quite feasible in affecting the end virus product.

hey sannica, thanks for your comment.

lets take a real exmple-aminoacyl-trna synthetase enzyme.

its need 3 site for its function:

a)binding site for atp
b)binding site for trna
c)binding site for amino acid

what comes first and what function it have?

we can also take the open circulatory system. what comes first: the heart, the vessels, or the blood?

i think i also have an interesting argument:

what if we will find a robot that make of dna?