From: bk186@cleveland.Freenet.Edu (Julie Thomas)
Subject: Re: Divergence of esterase genes
Reply-To: bk186@cleveland.Freenet.Edu (Julie Thomas)
Organization: Case Western Reserve University, Cleveland, OH (USA)
Date: Tue, 21 Jul 92 12:08:56 GMT




Michael first provided the typical story about how new genes are 
made: 

| Have you heard of pseudogenes? Let's imagine gene A to exist which 
| performs the vital function X. It duplicates into A and A'. Now 
| imagine that either one (let's say A') mutates and loses its ability 
| to do X. It is backed up by A!  Hence A'  becomes free to change even 
| further, as it is UNDER NO SELECTIVE PRESSURE TO remain 
| equivalent to A. A keeps on doing X. The rate of mutation in A' soars. 
| It might pick up a new function. It might indeed become utter junk. 
| It might fuse with a novel exon imparting a new composite function 
| X + Y.

I replied with some questions:

>That's a good synopsis of the standard story, but I've always 
>wondered about a few things.
>
>1.  As you noted, once the duplicated gene is no longer translated, 
>it becomes a pseudogene and can acquire changes apart from 
>selective constraint.  But what have we here?  Isn't this the old 
>story about new proteins evolving by chance?  Why yes it is.  
>Selection is no longer editing the creation of new proteins. In 
>essence, this scenario has proteins popping up by pure chance.  

Michael replied in turn:

| No: mutations are essentially chance events, but selection and
| evolution as processes are not driven by chance.

And it's my turn once again (and so goes the rest):

Yes, but the gene duplication/divergence story decouples mutation 
from selection/evolution.  The duplicated gene is not under 
selection, thus mutations which pop up will remain unless lost by 
drift.

| When you say "popping up by pure chance" you imply that it is
| unlikely. Remember the size of genomes, the plasticity of genomes, 
| the potential for duplication at various levels (intra-gene;
| chromosomal; whole genomic duplication etc); the presence
| of various mobile elements and so on. 

Are you suggesting that these processes make it LIKELY that a DNA 
sequence will randomly change to form a new, novel protein encoding 
fragment?  What is your evidence?

>2.  If this scenario is true, then we should find, in any genome, 
>some pseudogenes which encode new proteins.  That is, if the 
>pseudogene that has sufficiently diverged was cloned out and 
>placed under the control of some common promoter, and reinserted 
>back into the genome, we should see the expression of some protein 
>with a novel function.  Has this been done?  

| A point of definition, since my wording (above) was ambiguous: a
| pseudogene is *by definition* non-functional, derelicted to varying | degrees; for instance, ib the human globin family, of two known 
| pseudogenes, one has a frameshift  but is otherwise almost "wild 
| type"; another is totally wrecked, but it does maintain a TATA box 
| Therefore what you propose (reinserting the pseudogene next to a 
| functional promoter) is unlikely to give rise to full-length protein, 
| let alone a protein with a function.

I agree!!  But the gene duplication/divergence story implies that the 
genome should contain pseudogenes which do encode novel protein 
function.  You say it would be unlikely?  Recall what you wrote above:

| When you say "popping up by pure chance" you imply that it is
| unlikely. Remember the size of genomes, the plasticity of genomes, 
| the potential for duplication at various levels (intra-gene;
| chromosomal; whole genomic duplication etc); the presence
| of various mobile elements and so on. 

So, where are the pseudogenes with novel, functional gene products?

>
>3.  This process is quite slow.  If you look at the discarded portion 
>of the fibrinogens, it has been undergoing change at the rate of 1% 
>per 1.0 and 1.7 million years.  So how different must a protein be to 
>acquire a novel function?  Susumu Ohno thinks a reasonable guess is 
>25% on avergage.  That would mean this process would generate a 
>new gene from a pre-existing one in 25-42.5 million years.  (This 
>only accounts for primary sequence divergence, not the reactivation 
>of the new gene).  

| There are documented cases where a very small change can have a
| large effect on function. 

Yes, for example if an amino acid in the active site is changed to a 
different type of amino acid, you'll probably lose that function.

| In any case what you mention above is the rate of base 
| substitutions(correct me if I'm wrong). If we take into account 
| duplications,exon shuffling, transpositions etc, as being vital 
| determinantsof change, then the figure of (25-42.5) million years
| loses meaning; in any case, fibrinogens are only one example; and
| different types of protein evolve at different rates; I believe
| fibrinogen is relatively fast. But what species was the data derived 
| from? What is the generation time of that species? I would tend
| to be critical of the assertion "a reasonable guess is 25% on 
| average".

First, what was measured was the rate of amino acid substitution. 
The other processes ARE taken into account, for over evolutionary 
time, they could have and might have occurred.  Furthermore, if you 
desire to use another protein aside from fibrinogens, be my guest.  
Since fibrinogens are among the fastest of evolving proteins, it'll 
simply mean that it takes much longer than 42.5 million years to 
evolve a new protein.  As for the 25% figure, you might be right.  If 
you compare Neurospora cytochrome c with that from wheat, they 
differ by about 50%, yet both still function as cytochrome c.  

>4.  Three types of mutations can occur with single base substitions 
>in the coding  region:  no alteration in amino acid seqence; an amino 
>acid substitution; and premature termination.  The ratio of these 
>three types is 1: 2.7: 0.15 respectively.  That means, on average, 
>about one out of every 26 mutations will cause premature protein 
>termination.  Also, various other types of mutations are bound to 
>occur such as frameshifts which are the result of deletions and 
>insertions.  All in all, you have lot's of mistakes occuring without 
>nothing to edit them out of the gene pool.  

| What you are saying is that a large proportion of mutations
| knocks out a protein entirely. Ah, but when that occurs:
| if that change gives rise to a lethal mutant, it will be
| thrown into the dustbin by selection. If there is a suitable
| "back up" that gene could become a pseudogene (a "molecular
| fossil"). Selection is your "editor".

Yes, but you have uncoupled selction from the whole process.  Recall 
that the evolving gene is a pseudogene which has no function.  So 
how do you have a lethal mutation in sequence which has no 
function?  You don't.  Selection only works AFTER the gene is 
"reactivated".  And this is basically the scenario where you change a 
protein by chance in an "all at once" manner, and THEN see if it 
works in a novel and functional way.  

">5.  Finally, what of gene conversion?  Gene conversion is the non-
>reiprocal transfer of DNA sequence between 'homologous' sequence.  
>For example, A could serve as the template to transfer it's 
>sequence to A'.  How frequent is gene conversion as opposed to the 
>diverging force of mutation?  FAR more frequent (about 1000X more 
>frequent).Thus, divergence seems unlikely.  

| Remember we are talking about statistical figures here; not *all*
| mutations are succesfully edited. Moreover, the editing can go
| two ways: back to the original, or it can go the mutant's way;
| if I'm remembering correctly, the repair system has no in-built
| way of "knowing" which is the right sequence.

Sure, but once again this stuff is not applicable given the gene 
duplication/divergence story.  The whole point to the story is that 
you can keep the functional gene product at work while the 
duplicated one can change.  Well, that whole point to the story is 
lost if you are going to have the duplicated gene sequence convert 
the original one!  

| The mechanism you describe has been postulated to give rise to
| phenomena of "horizontal evolution" such as the uniformity
| of some spacer regions between some Xenopus rRNA genes.
 
Gene conversion is a very common phenomena.  

By the way, how can one falsify this gene duplication/divergence story?