Reanimating Extinct Genes

The dinosaurs are unlikely to have left us any of their genetic code – thankfully.
Credit: Smithsonian

The movie Jurassic Park was a lesson in how resurrecting extinct organisms can go awry. A new project plans to take a safer route: resurrect a single gene from an extinct species of bacteria. This tiny snippet of DNA will be implanted in modern-day bacteria, with the goal of seeing whether evolution can be replayed in the lab.

In previous work, paleogeneticist Eric Gaucher from the Georgia Institute of Technology and his colleagues reconstructed earlier forms of a common gene by computing the way different lineages diverged to create the bacterial family tree.

"It is a bit like what historical linguists do when they infer the spelling or pronunciation of an ancient word from its modern derivatives," Gaucher says. "Except, we are working with the DNA alphabet."

As part of NASA’s Astrobiology: Exobiology and Evolutionary Biology program, Gaucher and Betul Kacar, also from Georgia Tech, now plan to plug one of their reconstructed genes in a modern organism’s DNA.

If this genetic anachronism evolves forward along one of the branches that the researchers have computed, then this will provide some verification of this molecular genealogy technique, as well as give support to the notion that evolution is repeatable and not simply a matter of chance.

Ghosts in the code

It is hopeless to think that dinosaur DNA could be recovered from mosquito blood trapped in amber (or from anywhere else for that matter), as the molecular code isn’t likely to survive 65 million years.

Researchers have reconstructed most of the woolly mammoth’s DNA.

The chances are far better for more recent extinctions. A nearly complete DNA sequence of the woolly mammoth (which died out about 11,000 years ago) was published last November, giving some people ideas about bringing these giants back to life.

However, finding frozen hair and tissue samples is not the only way to isolate extinct DNA. Gaucher and his colleagues have shown that it is possible to estimate the genes that existed in long-dead organisms by doing a genetic survey of their family tree.

It is a bit like guessing what color your great-great-great grandmother’s eyes were by cataloguing the eye colors of all her living descendants and playing back the rules of inheritance. In the case of gene reconstruction, Gaucher’s team estimates the DNA code of an extinct life form by comparing the codes of its living descendants and using theories of genetic mutations.

In particular, the researchers looked at the gene for a protein called elongation factor (EF), which is vital for forming other proteins in cells. Specifically, EF shuttles amino acids (the protein building blocks) to the ribosome (the protein factory). All organisms from bacteria to humans have their own version of the EF protein.

The researchers compared the DNA of a large set of bacteria species. The 1200 base pairs that make up the EF gene were largely identical in the different species except for small mutations. Using their computational model, Gaucher and colleagues estimated in which common ancestor (which great-great-great grandmother bacteria) these mutations originated.

A protein thermometer

Evolution all over again? E. coli – seen here at 10,000x magnification – will have one of their genes swapped out for an ancient version.
Credit: USDA

Using the DNA sequences of past EF genes, the scientists recreated EF proteins that were in service millions of years ago. They found that these resurrected proteins worked best at different temperatures.

"They serve as a thermometer for the environment that the host organism lived in," Gaucher says.

The farther back in time the researchers looked, the hotter the EF proteins liked it. The oldest proteins in their study – corresponding to 3.5 billion years ago – preferred the highest temperatures of 73 degrees Celsius (160 degrees Fahrenheit). This matches some geologic evidence that indicates the average global temperatures in this time period were scorching hot.

The success of this gene reconstruction and protein resurrection is due to "the experimental tractability of [Gaucher’s] system, and the crucial role of elongation factors in cell function," says Belinda Chang of the University of Toronto, who is not involved in this work.

Sick with age

Gaucher and Kacar now plan to go to the next step: take an ancient EF gene, whose protein is most stable at 55 degrees Celsius, and insert it into a modern E. coli bacteria, whose optimal growth temperature is 37 degrees Celsius.

We tend to think of genetic modification being used to improve an animal or a plant, but in this case it will handicap these microbes with an outdated EF gene.

The elongation factor (EF) protein shepherds the parts needed to build other proteins.
Credit: David S. Goodsell of The Scripps Research Institute

"These bacteria are going to be sick," Gaucher says. Their EF protein will still shuttle amino acids to the ribosome, but not as effectively as before.

Like a molecular Rip Van Winkle, the ancient EF gene will feel strong evolutionary pressure to adapt to its new cooler surroundings. Mutations that bring the EF protein closer in-line with the 37 degree temperature will help certain E. coli outcompete their neighbors.

"It’s difficult to see evolution, short of building a time machine," Gaucher says, but their technique may be the next best thing.

Press replay

The scientists will be verifying whether the mutations in the E. coli’s EF gene follow the same path as was taken by the line of ancestor bacteria as they evolved over millions of years on the slowing cooling Earth.

The late paleontologist Stephen Jay Gould imagined doing a similar examination on a much broader scale.

"I call this experiment ‘replaying life’s tape.’ You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past… Then let the tape run again and see if the repetition looks at all like the original," Gould wrote in his 1989 book Wonderful Life.

Gould said that "any replay of the tape would lead evolution down a pathway radically different from the road actually taken." His hypothesis, that evolution is directed largely by chance rather than some ultimate goal of progress, has implications not only for our understanding of life on Earth but also for our search for life on other planets where the "tape recorder" may be completely different.

Gaucher’s group may be able to test whether Gould was right by following a few thousand generations of their modified E. coli over the next couple of years.

"I do believe that it is now possible, with tools that have recently been developed, to ‘replay the molecular tape of life,’ even if it is one (or a few) molecules at a time," Chang says.