Re: Duplicate genes that get modified to perform other functions.

• From: John Harshman <jharshman.diespamdie@xxxxxxxxxxx>
• Date: Thu, 02 Feb 2006 02:34:52 GMT

Elmer wrote:

> John Harshman wrote:
> 
>>Frank Sullivan wrote:
>>
>>
>>
>>>Thanks, John. I'll have to delve deeper into the AiG literature to find
>>>out why they don't consider these to be instances of mutation causing
>>>increased information.
>>>
>>>Perhaps they don't believe that evolutionist presumption that gene
>>>families are the result of duplication and modification, but it seems
>>>that it should be pretty easy to demonstrate that their similarities
>>>are non-random much in the same way you've done with the mtDNA
>>>sequences, only instead of showing common ancestry among different
>>>species, you'd have to show that the genes are homologous to one
>>>another, am I right?
>>
>>
>>Right. But of course AiG doesn't believe in the nested hierachy among
>>species, so why should they believe in the nested hierarchy among genes?
>>When you start out by rejecting the data, it's easy to reject the
>>conclusion. I suspect they would demand to see a duplicate produced in
>>real time, and then diverge in real time. And that's unlikely. Just like
>>they want to see a dog give birth to a cat, or a video of dinosaurs
>>morphing into birds. It's all a version of the "Were you there?" tactic.
>>
> 
> 
> This has been an interesting discussion. I ran across the following 
> while looking for something on gene duplication last night:
> 
> BMC Evol Biol. 2004 Mar 8;4:9. Upstream plasticity and downstream 
> robustness in evolution of molecular networks.By Maslov S, Sneppen K, 
> Eriksen KA, Yan KK. Department of Physics, Brookhaven National 
> Laboratory, Upton, New York 11973, USA.
> 
> BACKGROUND: Gene duplication followed by the functional divergence of 
> the resulting pair of paralogous proteins is a major force shaping 
> molecular networks in living organisms. Recent species-wide data for 
> protein-protein interactions and transcriptional regulations allow us to 
> assess the effect of gene duplication on robustness and plasticity of 
> these molecular networks. RESULTS: We demonstrate that the 
> transcriptional regulation of duplicated genes in baker's yeast 
> Saccharomyces cerevisiae diverges fast so that on average they
> lose 3% of common transcription factors for every 1% divergence of their 
> amino acid sequences.

This means that the two promoter regions upstream of the protein-coding
genes are evolving so as to change the binding sites for transcription
factors. Transcription factors are proteins that bind to the promoter
region so as to increase or decrease the rate of transcription.
Different transcription factors are produced in different tissues at
different times (because their transcription is controlled by other
transcription factors). If a transcription factor no longer binds to the
promoter, that changes the expression pattern of the gene. So the
duplicates are ending up with different expression patterns, whether
temporal, tissue-specific, or both.

> The set of protein-protein interaction partners of 
> their protein products changes at a slower rate exhibiting a broad 
> plateau for amino acid sequence similarity above 70%.

Proteins bind to other proteins and affect their activity. If this
changes, patterns of activity change.

> The stability of 
> functional roles of duplicated genes at such relatively low sequence 
> similarity is further corroborated by their ability to substitute for 
> each other in single gene knockout experiments in yeast and RNAi 
> experiments in a nematode worm Caenorhabditis elegans. We also 
> quantified the divergence rate of physical interaction neighborhoods of 
> paralogous proteins in a bacterium Helicobacter pylori and a fly 
> Drosophila melanogaster. However, in the absence of system-wide data on 
> transcription factors' binding in these organisms we could not compare 
> this rate to that of transcriptional regulation of duplicated genes. 
> CONCLUSIONS: For all molecular networks studied in this work we found 
> that even the most distantly related paralogous proteins with amino acid 
> sequence identities around 20% on average have more similar positions 
> within a network than a randomly selected pair of proteins. For yeast we 
> also found that the upstream regulation of genes evolves
> more rapidly than downstream functions of their protein products.

Thus changes in expression patterns, not changes in the proteins
themselves, are the major engine of evolution. That fits the
conventional wisdom.

> This
> is in accordance with a view which puts regulatory changes as one of the
> main driving forces of the evolution. In this context a very important
> open question is to what extent our results obtained for homologous 
> genes within a single species (paralogs) carries over to homologous 
> proteins in different species (orthologs).

Bet it does.

> I *think* I have an idea what's being said here, but I'd love to hear 
> comments from those with quite a bit more expertise than I have in this 
> subject.
> 

.

• References:
  • Duplicate genes that get modified to perform other functions.
    • From: Frank Sullivan
  • Re: Duplicate genes that get modified to perform other functions.
    • From: John Harshman
  • Re: Duplicate genes that get modified to perform other functions.
    • From: Frank Sullivan
  • Re: Duplicate genes that get modified to perform other functions.
    • From: John Harshman
  • Re: Duplicate genes that get modified to perform other functions.
    • From: Elmer

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