Gene Genesis: Scientists Observe New Genes Evolving from Mutated Copies

Researchers have observed in an experiment the exact steps bacterial genes take to evolve a new ability, unexpectedly adding a new twist on an old model

Christian Holmér (CC) via flickr

The history of life on Earth has been marked by the evolution of new genes—humans clearly have more genes with more diverse functions than do amoebas. So where do these additional genes, with their new roles, come from? Analysis of genomes shows that the duplication and modification of existing genes seems to be a major avenue for such innovation.

Conventional wisdom had it that duplicate genes provide raw material for evolution. The original gene continues to do its job, whereas the other copy is free to evolve in a different direction.

For example, the venomous cocktail delivered by a platypus's spurs includes three peptides remarkably similar to an antimicrobial compound used in the critter's immune system. The venom molecules evolved from duplications of the gene that codes for an immune compound. Scientists refer to groups of similar genes with different functions as families. Humans carry duplications, too—a group of molecules in the back of the eye that react to incoming photons of light hail from the family of opsin genes. Duplicate genes in the human genome were likely key during divergence from our common ancestry with chimps.

The idea that gene duplication could result in genes with new functions has been around for awhile. Geneticist Susumu Ohno explained the theory in detail in 1970. He argued that duplication is the most important evolutionary force—more powerful than genetic drift, for example. Scientists are still working out the specifics because the vast majority of mutations eventually arising in the duplicates are harmful, meaning they result in function loss; the duplicates would need to stick around for generations before acquiring helpful mutations. But the model required that natural selection should spare the extra gene copies until they had a chance to change for the better.

This problem bothered Dan Andersson, a microbiologist at Uppsala University in Sweden, and John Roth, a geneticist at the University of California, Davis. To better explain how new genes could evolve they suggested a modification of the old model: instead of waiting around for a beneficial mutation, perhaps the beneficial mutation comes first.

This model takes note of the fact that many genes do their primary job of coding for a particular protein very well, but also have a weak secondary function that may become important under certain environmental stressors. For example, one gene might code for a protein that helps bacteria gobble glucose, but also allows the bacteria to snack on starchy cellulose. If all sugar disappears from its environment and only cellulose remains, the bacteria that have this gene will have the capacity to eat more cellulose and therefore be selected for over time and endure. Andersson and Roth's model posited that beneficial mutations already present by chance would be favored by natural selection and stick around in the genome. When the gene is amplified through the duplication, the extra copies give rise to new genes that are better at performing the secondary function, thereby making it prime. "The key is that it never goes off selection," Roth says.

In a study in the journal Science, Andersson, Roth and their colleagues demonstrate the process in lab-grown Salmonella enterica. They grew one strain missing a gene key for expressing the essential amino acid tryptophan. The strain needed to rely on another gene, which had a primary job but also a weak ability to take on the missing gene's work. The researchers encouraged the bacteria to duplicate the overworked gene, and its copies gathered mutations—some of which enhanced tryptophan production. At the end of a year's time (3,000 generations later) the bacteria had one gene that did the original job and a second that had evolved a new primary function—manufacturing tryptophan.

Prior to this study, scientists have relied on more theoretical approaches such as bioinformatics to infer how new genes arise. Now they have demonstrated the evolution of a new gene experimentally. The team published their results on October 19.

The model explains how novelty is generated in evolution, which is "tremendously exciting," says Gavin Conant, an evolutionary biologist at the University of Missouri—Columbia who was not involved in the study. Whether the model will apply to organisms other than bacteria remains to be seen, but Conant says he would be very surprised if researchers do not eventually find the process in other systems. "They have a step-by-step documentation of the model, essentially proof that this can happen," he says.

Conant points out that we cannot hope to stay 40 years ahead of microbes when they can evolve new abilities in just a few years. But microbes aren't always working against us. If the model holds, it can give researchers insight to harnessing evolution's power—as bioengineers coax microbes to gobble oil spills, for example. Says Conant of the genome’s innovative abilities: "It reminds us again of just how powerful evolution is in microbes."

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