Errors in protein structure sparked evolution of biological complexity

May 18, 2011

Over four billion years of evolution, plants and animals grew far more complex than their single-celled ancestors. But a new comparison of proteins shared across species finds that complex organisms, including humans, have accumulated structural weaknesses that may have actually launched the long journey from microbe to man.

The study, published in Nature, suggests that the random introduction of errors into proteins, rather than traditional natural selection, may have boosted the of biological complexity. Flaws in the "packing" of proteins that make them more unstable in water could have promoted interactions and intracellular teamwork, expanding the possibilities of life.

"Everybody wants to say that evolution is equivalent to natural selection and that things that are sophisticated and complex have been absolutely selected for," said study co-author Ariel Fernández, PhD, a visiting scholar at the University of Chicago and senior researcher at the Mathematics Institute of Argentina (IAM) in Buenos Aires. "What we are claiming here is that inefficient selection creates a niche or an opportunity to evolve complexity."

"This is a novel bridge between protein chemistry and evolutionary biology," said co-author Michael Lynch, PhD, professor of biology at Indiana University. "I hope that it causes us to pause and think about how evolution operates in new ways that we haven't thought about before."

When mildly negative mutations arise in a species with a large population, such as the trillions of bacterial organisms that can fill a small area, they are quickly cleared out by selective forces. But when a new mutation appears in a species with a relatively small population, as in large mammals and humans, selection against the error is slower and less efficient, allowing the mutation to spread through the population.

To look at whether these mild defects accumulate in species with small populations, Fernández and Lynch compared over 100 proteins shared by 36 species of varying population size. Though these shared, "orthologous" proteins are identical in shape and function, genetic differences alter them in more subtle ways.

Fernández and Lynch focused on design flaws called "dehydrons," sites where the protein structure is vulnerable to chemical reactions with water. Proteins with more dehydrons are more "unwrapped" - unstable in an aqueous environment, and therefore prone to bind with another protein to protect their vulnerable regions.

A computational analysis of 106 orthologous proteins confirmed their hypothesis that proteins from species with smaller populations were more vulnerable in water. The result suggests that structural errors accumulate in large organisms such as humans due to random genetic drift.

"We hate to hear that our structures are actually lousier," Fernández said. "But that has a good side to it. Because they are lousier, they are more likely to participate in complexes, and we have a much better chance of achieving more sophisticated function through teamwork. Instead of being a loner, the protein is a team player."

On their own, these unstable proteins might be expected to perform their cellular duties more poorly, possibly causing harm to the organism. But unstable proteins are also "stickier," more likely to form associations with other proteins that could introduce more flexibility and complexity into the cell. If these complexes create a survival advantage for the organism, forces of should take over and spread the new protein complex through the population.

"It's not an argument against selection, it's an argument for non-adaptive mechanisms opening up new evolutionary pathways that wouldn't have been there before," Lynch said. "It's those first little nicks getting into the protein armor that essentially open up a new selective environment."

To confirm that the accumulation of structural flaws in proteins preceded, rather than resulted from, the formation of complexes, Fernández and Lynch turned to a natural experiment. Some bacterial species have two types of populations: communities that live inside other and larger populations living free in the environment. When orthologous proteins were compared between these two populations, the same pattern emerged – proteins from the smaller populations were more flawed than those from the free-living bacteria of the same species.

Despite these accidental benefits, the accumulation of too many structural flaws can be dangerous to an organism. When highly reactive proteins such as prions, amyloid-beta, or tau are too sticky, they can clump into aggregates that kill cells and cause diseases such as Alzheimer's and encephalopathy.

The implication that complexity initially arose by accident may be provocative within the field of evolutionary biology, the authors said. The discovery that flawed proteins are more likely to form complexes could also revolutionize the growing field of bioengineering, where the tools of evolution are used to create stronger, self-assembling, or self-reparing materials.

"Natural designs are often one notch more sophisticated than the best engineering," Fernández said. "This is another example: Nature doesn't change the molecular machinery, but somehow it tinkers with it in subtle ways through the wrapping."

Explore further: Human sense of fairness evolved to favor long-term cooperation

More information: "Nonadaptive origins of interactome complexity," Nature, May 18 2011. doi: 10.1038/nature09992

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210
not rated yet May 25, 2011
I like this! A REASONABLE argument for AND against a widely held concept or two: "When mildly negative mutations arise in a species with a large population, such as the trillions of bacterial organisms that can fill a small area, they are quickly cleared out by selective forces. But when a new mutation appears in a species with a relatively small population, as in large mammals and humans, selection against the error is slower and less efficient, allowing the mutation to spread through the population." Now, a NON-random mutation, one introduced say, by man during his attempts to genetically engineer food could easily stress the selection process; that is, speed it up or escape it completely - this is the power humanity has FOR EXAMPLE. Now, Nature has a tool bag that comes with a correction trigger, an event or chain of events causes that bag of tricks to open and say' gene pool ONE share recombinantly some of your gene pool with gene pool TWO. Infection is another tool.
210
not rated yet May 25, 2011
"It's not an argument against selection, it's an argument for non-adaptive mechanisms opening up new evolutionary pathways that wouldn't have been there before,"
Hence, science does reasonably acknowledge ADAPTIVE MECHANISMS in the ebb and flow of evolution. Mutation is there, mutation is change BUT IT IS NOT THE WHOLE STORY! A male black widow spider (A) mates, gets eaten by the female(B): his gene pool is now expressed in his offspring as AB he's done! Those offspring may be super spiders but the super-super-spider that would have been expressed by a mating of him(A) and a (K), had he lived, will never be seen unless a male (AB) finds (K) before she dies. If (A) acquired his super-power (resistance to DDT) through a damaged protein, via a progenitor or vector, a non-random mutation (manmade -human introduced) will probably have a whole generation of super-spiders (locally or globally)thru same mechanism. Selection? Mutant may or may not able to mate. EXCELLENT ARTICLE!!!
Ethelred
5 / 5 (1) May 26, 2011
Hence, science does reasonably acknowledge ADAPTIVE MECHANISMS in the ebb and flow of evolution.
Has since Darwin.

Mutation is there, mutation is change BUT IT IS NOT THE WHOLE STORY!
Yes. Known since genes and mutations were discovered and before. Since Darwin and Wallace. Its called Natural Selection.

A male black widow spider (A) mates, gets eaten by the female(B): his gene pool is now expressed in his offspring as AB he's done!
Yes. Except his genes aren't done.

(A) and a (K), had he lived, will never be seen unless a male (AB) finds (K) before she dies
Sure. Evolution is a process that works with what is not with what could have been.

Selection? Mutant may or may not able to mate.
That is part of selection.

Ethelred
Ethelred
3 / 5 (2) May 26, 2011
published in Nature, suggests that the random introduction of errors into proteins, rather than traditional natural selection, may have boosted the evolution of biological complexity
Which is nonsense since Natural Selection is dependent on mutations. This is what happens when people write articles about subjects they don't know.

Flaws in the "packing" of proteins that make them more unstable in water could have promoted protein interactions and intracellular teamwork, expanding the possibilities of life
Which is still mutation followed by selection.

"Everybody wants to say that evolution is equivalent to natural selection
I never said that and its the first time I have run across it.

Ariel Fernández, PhD, a visiting scholar at the University of Chicago and senior researcher at the Mathematics Institute of Argentina
I see. Not a biologist or a paleontologist who would know better than to make such ludicrous claims about how evolution is supposed to work.>>
Ethelred
3.5 / 5 (2) May 26, 2011
"What we are claiming here is that inefficient selection creates a niche or an opportunity to evolve complexity."
Well that is different from the nonsense before. Selection can't be efficient all the time. That is why there are founder effects.

But when a new mutation appears in a species with a relatively small population, as in large mammals and humans, selection against the error is slower and less efficient, allowing the mutation to spread through the population.
This is covered by the founder effect. It is NOT new.

A computational analysis of 106 orthologous proteins confirmed their hypothesis that proteins from species with smaller populations were more vulnerable in water.
Do they know that the proteins were encoded in the DNA? It is in the DNA where the mutations occurred. And yes smaller populations should have more odd stuff going on.>>
Ethelred
3 / 5 (2) May 26, 2011
humans due to random genetic drift.
Gosh. There is a name for that. Its called ... Genetic Drift. Amazing! They have discovered a long known part of the evolutionary process. A stunning achievement to rediscover that which was not lost. I suppose they managed it by not studying the field.

spread the new protein complex through the population.

"It's not an argument against selection, it's an argument for non-adaptive mechanisms opening up new evolutionary pathways that wouldn't have been there before,"
Also known as Hopeful Monsters.

"This is another example: Nature doesn't change the molecular machinery, but somehow it tinkers with it in subtle ways through the wrapping."
Or through the molecular machinery via mutations of the DNA. Where the hell did he think the proteins are encoded anyway? In magic land? Maybe it's just sloppy writing.>>
Ethelred
3.5 / 5 (2) May 26, 2011
This interesting research results interpreted by people that apparently didn't know about

Hopeful Monsters
Genetic Drift
Founder Effects
Mutation followed by Natural Selection

Basically they came into an area of science without learning what was already known and thus they 'discovered' stuff that was fairly well understood already.

Ethelred
210
not rated yet May 27, 2011
"I see. Not a biologist or a paleontologist who would know better than to make such ludicrous claims about how evolution is supposed to work"

Oh, hey, let us pass all the blame where it is due. The principal researcher had a bit of help -
"This is a novel bridge between protein chemistry and evolutionary biology," said co-author Michael Lynch, PhD, professor of biology at Indiana University. "I hope that it causes us to pause and think about how evolution operates in new ways that we haven't thought about before."
See ethey, he had help and IT WAS a biologist. I was able to contact the university, the university of Indiana and yes he works there and believe it or not, they had the usual help from grad students,in fact there were MANY sets of eyeballs looking at this thing and I did direct him to your comments. Ethey, I am sure you know more than most just where they all went wrong -get them on the phone and SET-EM-STRAIGHT!
Oh, and,
WORD-TO-YA-MUTHAS