Fitting in: Newly evolved genes adopt a variety of strategies to remain in the gene pool

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Eureka Alert

The largest-ever experimental analysis of duplicated genes provides insight into mechanisms of evolution

Zürich, Switzerland – When Mother Nature creates an identical copy of a gene in an organism’s genome, the duplicated copy is usually deleted, inactivated, or otherwise rendered nonfunctional in order to prevent genetic redundancy and to preserve biological homeostasis. In some cases, however, gene duplicates are maintained in a functional state. Until now, the biological and evolutionary forces behind the maintenance of these duplicates as functional components of the genome have remained unclear.

To determine the basis for the persistence of functional gene duplicates in the genome, three scientists at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich have collaborated on the largest systematic analysis of duplicated gene function to date. Using an integrative combination of computational and experimental approaches, they classified duplicate pairs of genes involved in yeast metabolism into four functional categories: (1) back-up, where a duplicate gene copy has acquired the ability to compensate in the absence of the other copy, (2) subfunctionalization, where a duplicate copy has evolved a completely new, non-overlapping function, (3) regulation, where the differential regulation of duplicates fine-tunes pathway usage, and (4) gene dosage, where the increased expression provided by the duplicate gene copy augments production of the corresponding protein.

Their results, which appear in the October issue of the journal Genome Research, indicate that no single role prevails but that all four of the mechanisms play a substantial role in maintaining duplicate genes in the genome.

“Our results contradict other recent publications that have focused on a single selective pressure as the basis for the retention of gene duplicates,” explains Dr. Uwe Sauer, principal investigator on the project and Professor at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich. “We show that, at least for yeast metabolism, the persistence of the duplicated fraction of the genome can be better explained with an array of different, often overlapping functional roles.”

Yeast metabolism provides an ideal model for investigating the functional basis for gene duplication because a large proportion of genes involved in this biological process have been duplicated. Of the 672 genes involved in yeast metabolism, 295 genes can be classified into 105 families of duplicates. To put this into perspective, the yeast genome has an estimated total of 6,000 genes, 1,500 of which are considered to be duplicates. An ancient whole-genome duplication event is thought to be responsible for the formation of many of these duplicate copies.

Sauer’s group demonstrated that of the 105 families of duplicated gene families involved in yeast metabolism, 34 demonstrated back-up function, 19 were involved in increased gene dosage, 18 exhibited regulatory functions, and 18 had evolved new, more specialized functions. Therefore, each of these mechanisms plays a substantial and important role in the maintenance of functional duplicates in the gene pool.

12 Comments

When Mother Nature creates…

Ohhh, an instance of Intelligent Design Creationism in action, is it? This paper is going in the list of scientific ID publications. *L*

Wait - so ‘mutations’ can result in new genetic information! But…but then…evolution can explain the diversity of life!

I’ve been so blind!

And now, the whole fascinating world of biology is open to my no longer conflicted mind! Instead of spinning endless tormented, obsessive, irrational spiels to deny reality, I can actually learn something!

Sorry - just kidding - I’ve never been a creationist. However, who knows, maybe some of them will respond this way.

In another groundbreaking development, a test for intelligent design has finally been proposed, in panel 5 of this week’s “Tom Tomorrow” cartoon. It’s well, well worth the brief wait through a movie commercial. http://www.salon.com/comics/tomo/20[…]/index1.html

Hot damn, I knew there was a reason I ultimately gravitated toward yeast genetics. The work coming out on the1 yeast whole-genome duplication event (such as last year’s Nature paper) has completely lit my interest in a way that lipid biochemistry (my second choice) hasn’t in a long while.

Still not going to convince me not to leave the bench behind, though.

Good points all - I haven’t actually read Demski’s books, but I’ve heard he has some sort of thermodynamic argument that information cannot be created or whatnot. However, gene duplication followed by mutation is clearly a way for a new gene to be created. The “information” or “complexity” increases, but I don’t see how one justifies the claim this is against some physical principle. Anyway, Minimalist, I can’t believe that lipid biochemistry isn’t exciting for you anymore (sarcasm). But if I read the news story right, the experiment described in this thread did involve actual benchwork. Bioinformatics has advanced far, but we are far from being able to do everything in silico yet.

Good points all - I haven’t actually read Demski’s books, but I’ve heard he has some sort of thermodynamic argument that information cannot be created or whatnot.

Once again, it should be pointed out explicitly that this “mutations can’t produce new information” BS is standard ICR boilerplate from 30 years ago.

Once again, we see that ID simply has nothing new to say. Same old wine, shiny new bottle. (shrug)

If you want to see what I’ve had to put up with from the IDist crowd, give this a read:

http://telicthoughts.com/?p=292#more-292

Eric Murphy -

The whole obsession with the words “random and undirected” is simplistic and unsophisticated.

Evolution is the result of genetic variability, usually when it is acted on by natural selection. Natural selection is certainly necessary for the highly specialized, massively diverse life we see today. Technically, genetic variability alone can produce some evolution.

We often use the term “mutation” to refer to any event that creates genetic diversity. This can be confusing, because the same word is used in related but slightly different ways in other scientific contexts - in medicine, for example, “mutation” is often short-hand for a genetic feature associated with an illness phenotype. In this message, when I say “mutation”, I mean any event that produces genetic variability.

Mutation in this sense is the inevitable result of any genetic reproduction (including, within multicellular organisms, mitotic reproduction of non-germ line cells). The genome of a non-reproducing cell can undergo “mutation” as well, albeit at a far lower “velocity”. Is it random and undirected?

Yes, mutation is usually “random” in the sense that it is not guided by an apparent “goal”. Science does not conjecture that a colon epithelium cell “decides” to become pre-cancerous as it replicates its DNA, for example, nor that a sperm cell of an ancient frog ancestor might have “decided” to change its DNA sequence in a conscious effort to “code for” better jumping muscles. Rather, we accept the overwhelming evidence that these things occur as a result of the underlying nature of the physical universe, the same way other “spontaneous” physical and chemical events occur.

“Random” is a profound word, however, in a league with “infinite”, “probable”, “deterministic”, etc. It is a word whose meaning is not easily pinned down with precision. Yes, I realize that “Webster’s” surely has a definition, but that’s not my point. Ionizing radiation can increase the mutation rate. Not only that, but some base pairs are more likely to be “mutated” than others when exposed to higher-than-usual doses of some types of radiation. However, it is still, to human eyes, random at the level of the individual base pair or base sequence. A statistician would point out that this is merely a “weighted probability” situation - some outcomes have a stronger probability than others. A quantum physicist, or another statistician, might point out that when you sum up enough seeming “random” events, the outcome appears very “planned” or “deterministic”. So it’s fair to say that “mutations” occur “randomly”, but it’s not as straightforward a statement as it may sound on the surface.

Natural selection is absolutely non-random. However, it can only act on phenotypes; phenotypes determined by underlying genetic information, among other things. But did the environmental pressures which act on phenotypes arise “randomly”? It’s ultimately a non-answerable, and perhaps meaningless question.

As usual, creationists are, as I said above, spinning endless tormented, obsessive, irrational spiels to deny reality.

It’s amusing to note that there are no creationists in this thread. That’s because the lead-in article is about science, not court rooms or religious issues.

Harold: all good points. I’m not a mathematician myself (to put it mildly), but I’m pretty sure I’ve read in various places that a) it’s very difficult to prove “randomness” in a formal sense, and b) “random” will have different formal meanings in different contexts, e.g., information theory, quantum physics, probability theory, etc.

All that aside, I think where creationists draw the line is their flat refusal to believe that any “non-directed” process, random or otherwise, can produce biological novelty. As you can see from following the link I provided, there is simply no amount of evidence that non-teleological processes can produce biological novelty that will ever convince them.

So eventually arguing with them becomes pretty thin entertainment. :-)

Fitting in: Newly evolved genes adopt a variety of strategies to remain in the gene pool

Various genes have been spotted using freestyle, breast stroke, back stroke, butterfly and deep diving. A variant of the sperm whale myoglobin gene said, “It helps to be able to hold your breath for a long time.”

So to find the 35 genes that had back up function did these guys have to mess up the primary gene in each of the 105 duplicated gene pairs and see if the other one would activate? Or is it a deal where with a million yeast in a dish you can usually just find one that already has a damaged primary and just observe whether the secondary is filling in?

I can’t believe it, my co-worker just bought a car for $50843. Isn’t that crazy!

I can’t believe it, my co-worker just bought a car for $50843. Isn’t that crazy!

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This page contains a single entry by PvM published on October 3, 2005 1:09 PM.

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