Experiment documents evolution of genome in near-real time

[RichardPrins]

Researchers identified all the changes in a bacterium's complete set of genes during a 44-day evolution experiment

A team led by bioengineering researchers at UC San Diego report in the November issue of Nature Genetics rapid evolutionary changes in a bacterial genome, observed in near-real time over a few days. Scientists have previously published static "snapshots" of the genome sequences of more than 100 bacterial species, from the harmless to those that cause plague, but this new report shows how these genomes are moving targets.

"Paleontologists look at the fossil record to study how evolution of dinosaurs and other animals occurred over millions of years, but in the case of the E. coli bacterium, new technology has given us the ability to observe evolution as it is occurring over a matter of days," said Bernhard Ø. Palsson, the senior author of the study and professor of bioengineering at UCSD. "The published genomic sequences of bacteria are like a fossil record and our experiments confirm that these genomes can change quickly as bacteria adapt to new conditions."

Because of past technical limitations, biologists have historically made inferences about rapid bacterial evolution by carefully observing changes in a handful of genes at a time or by monitoring the visible characteristics, or phenotypes, as the organisms adapt. Palsson's team used comparative genome sequencing technology developed by NimbleGen Systems Inc., a Madison, WI-based biotech firm, to identify changes that occurred during the experiment in the bacterium's complete set of genes.

In a paper scheduled for online publication Nov. 5 on Nature Genetics's Website, the researchers report that they grew E. coli in an environment that favored the emergence of mutants: the organism was fed a poorly metabolized carbon and energy source called glycerol. The researchers removed samples of cells from the culture and sequenced their entire genomes as a way to find mutations that enabled faster growth.

After six days of growth, mutations appeared in the gene for an enzyme that initiates the process of enzymatically breaking down glycerol. Cells with mutations in the so-called glycerol kinase gene grew 20 to 60 percent faster than those without the mutation.

Mutations also appeared in a second, unrelated gene for an enzyme called RNA polymerase. "That was a surprise to almost everybody because RNA polymerase is involved in one of the core processes of any cell," said Palsson. "You wouldn't expect that gene to change because a wide variety of cellular process would be affected; it's like replacing the wiring system in a building when a light bulb burns out. But we repeated the experiment more than 50 times and mutations in the RNA polymerase gene appeared again and again."

The researchers report that mutations in both genes appeared together in several cases after six to eight days in the glycerol-based cultures, and E. coli cells containing both mutated genes grew 150 percent faster than the starting strain of E. coli. To confirm that the mutants were indeed responsible for the faster growth, the researchers substituted the two mutant genes into the original strain and duplicated the faster growth rate. "We expected to find many mutated genes and we thought our results would be very difficult to understand, but neither was the case," said Christopher D. Herring, a co-author of the paper and a former member of Palsson's team who is now a research scientist at Mascoma Corp. in Lebanon, NH.

All the mutants arose in the experiments presumably as the result of naturally occurring errors in copying DNA into daughter cells during cell division. The precise changes in the sequence of DNA subunits were determined with comparative genomic sequencing technology from NimbleGen Systems, and further analyzed with technology from Sequenom Inc., a San Diego-based biotech company.

"This straightforward approach to the study of experimental evolution can be used as a tool for discovery and analysis, and could even be used to discover bacterial capabilities that would benefit humankind in a variety of ways," said Herring. "There may be a number of biotech companies that want to use this new approach to help design bacteria to do useful jobs."

UCSD's office of Technology Transfer and Intellectual Property Services has filed U.S. patent applications related to the experimental evolution approach. The approach combines computer modeling techniques with evolutionary design processes to optimize bacteria to perform commercially important processes. Aside from its commercial potential, experimental evolution of bacterial strains is also useful for refining the theory of evolution and the related process of natural selection of individuals with traits that convey a selective survival advantage. "Opinion surveys indicate that many people don't believe that evolution occurs," said Herring, "but if the skeptics could witness evolution actually occurring, as we did, I think they'd be more likely to believe that it's not just a theory."

[waveParticle]

Very interesting article. I'm out of my league here but what do think we're likely to changes in other more complex species that we can track with genetic sequencing?

[Vicki B]

I'm out of my league too, but it's amazing what you can patent these days huh?

Fascinating stuff though. Makes you wonder whether people who don't believe in evolution are not worried about bird flu evolving into something capable of wiping out a sizable number of humans...

[waveParticle]

I'm out of my league too, but it's amazing what you can patent these days huh?

Fascinating stuff though. Makes you wonder whether people who don't believe in evolution are not worried about bird flu evolving into something capable of wiping out a sizable number of humans...

Yep, it does. Fortunately for them some of the fellow members of their species do believe in evolution and are able to come up with appropriate interventions!

[Vicki B]

Another nice example of evolution in action is the peppered moth story, a n ice back-and-forth in evolution over the last couple of centuries. Not quite as spectacular as the article above but thought I'd post it anyway, although many people here are probably already familiar with it.

Short excerpt from Wikipedia:
"The evolution of the Peppered Moth over the last two hundred years has been studied in detail. Originally, the vast majority of peppered moths had light coloration, which effectively camouflaged them against the light-colored trees and lichens which they rested upon. However, due to widespread pollution during the Industrial Revolution in England, many of the lichens died out, and the trees which peppered moths rested on became blackened by soot, causing most of the light-colored moths, or typica, to die off due to predation. At the same time, the dark-colored, or melanic, moths, carbonaria, flourished because of their ability to hide on the darkened trees.

Since then, with improved environmental standards, light-colored peppered moths have again become common, but the dramatic change in the peppered moth's population has remained a subject of much interest and study, and has led to the coining of the term industrial melanism to refer to the genetic darkening of species in response to pollutants. As a result of the relatively simple and easy-to-understand circumstances of the adaptation, the peppered moth has become a common example used in explaining or demonstrating natural selection to laypeople and classroom students."

The rest is on http://en.wikipedia.org/wiki/Peppered_moth and everywhere else on Google for that matter, but as it's touted as an example of natural selection it does nicely emphasise natural selection in response to rapid human-induced change (or any other string selection pressure, for that matter). I'm sure there are loads of other similar examples in response to rapid climate change too.

[waveParticle]

Another nice example of evolution in action is the peppered moth story, a n ice back-and-forth in evolution over the last couple of centuries. Not quite as spectacular as the article above but thought I'd post it anyway, although many people here are probably already familiar with it.

Short excerpt from Wikipedia:
"The evolution of the Peppered Moth over the last two hundred years has been studied in detail. Originally, the vast majority of peppered moths had light coloration, which effectively camouflaged them against the light-colored trees and lichens which they rested upon. However, due to widespread pollution during the Industrial Revolution in England, many of the lichens died out, and the trees which peppered moths rested on became blackened by soot, causing most of the light-colored moths, or typica, to die off due to predation. At the same time, the dark-colored, or melanic, moths, carbonaria, flourished because of their ability to hide on the darkened trees.

Since then, with improved environmental standards, light-colored peppered moths have again become common, but the dramatic change in the peppered moth's population has remained a subject of much interest and study, and has led to the coining of the term industrial melanism to refer to the genetic darkening of species in response to pollutants. As a result of the relatively simple and easy-to-understand circumstances of the adaptation, the peppered moth has become a common example used in explaining or demonstrating natural selection to laypeople and classroom students."

The rest is on http://en.wikipedia.org/wiki/Peppered_moth and everywhere else on Google for that matter, but as it's touted as an example of natural selection it does nicely emphasise natural selection in response to rapid human-induced change (or any other string selection pressure, for that matter). I'm sure there are loads of other similar examples in response to rapid climate change too.

Yes, I have heard about this moth as an example of adaptation in a very short period of time. I can imagine that over an even longer period of time the species begin to diverge and are no longer able to interbred. It's really quite difficult for some people to imagine the immense period of time life has been on this planet. Life has had a very long time to try out different forms. I'm thinking of the varieties of sharks that once roamed the oceans billions of years ago. Some very strange sharks! I also find it utterly amazing the adaptations that many life forms have taken...bugs that look like sticks or leaves, flowers that make incredible aromas to attract pollinators, tails that break off of lizards and continue to squirm to throw off predators...oh geez, it goes on and on. It is really quite stunning how adaptable this genetic "code base" is.

[stipe]

After six days of growth, mutations appeared in the gene for an enzyme that initiates the process of enzymatically breaking down glycerol. Cells with mutations in the so-called glycerol kinase gene grew 20 to 60 percent faster than those without the mutation.

Mutations also appeared in a second, unrelated gene for an enzyme called RNA polymerase. "That was a surprise to almost everybody because RNA polymerase is involved in one of the core processes of any cell," said Palsson. "You wouldn't expect that gene to change because a wide variety of cellular process would be affected; it's like replacing the wiring system in a building when a light bulb burns out. But we repeated the experiment more than 50 times and mutations in the RNA polymerase gene appeared again and again."

its not evolution. the responses of bacteria to given environments is always the same. its an internal piece of code each cell has that helps them survive.

how can they call it a mutation when it happens the same way every time, probably in the same timeframe too..

[The Paul]

the responses of bacteria to given environments is always the same.

Yeah, they always either die, form a spore, or rapidly evolve with their high mutation rate and generation time somewhere around twenty minnutes to half an hour

Read a book.

[stipe]

the responses of bacteria to given environments is always the same.

Yeah, they always either die, form a spore, or rapidly evolve with their high mutation rate and generation time somewhere around twenty minnutes to half an hour
Read a book.

i did.

why would a mutation always produce the same result in the same timeframe?

which is more likely:
that random mutation produces the same result in the same timeframe every time, or
that an inherent trait instructs cells how to act in given environments.

when the people studying this experiment dont know what is responsible for the change, which would you consider a more reasonable explanation?

[RichardPrins]

why would a mutation always produce the same result in the same timeframe?

which is more likely:
that random mutation produces the same result in the same timeframe every time, or
that an inherent trait instructs cells how to act in given environments.

when the people studying this experiment dont know what is responsible for the change, which would you consider a more reasonable explanation?

they grew E. coli in an environment that favored the emergence of mutants: the organism was fed a poorly metabolized carbon and energy source called glycerol. The researchers removed samples of cells from the culture and sequenced their entire genomes as a way to find mutations that enabled faster growth.
...
All the mutants arose in the experiments presumably as the result of naturally occurring errors in copying DNA into daughter cells during cell division.

They do know what is responsible for the change. Most likely there were different types of mutants which were then all sequenced and from which the deduction was made. The same thing works with using radiation to create mutants as has been done in the past. The mutants may differ.