Biochemists reconstruct ancient protein, which suggests hot world

CHAPEL HILL -- A billion years ago, ancestors of today’s bacteria thrived in an environment similar to a Yellowstone hot spring, suggesting Earth may have been a much warmer place closer to the time when life originated.

Universities of Florida and of North Carolina at Chapel Hill scientists have used new techniques of "paleochemistry" to reconstruct ancient bacterial proteins based on similarities in the genetic sequences of modern proteins. The resurrected proteins proved most stable and functional at temperatures between 130 and 150 degrees Fahrenheit, implying that ancient bacteria lived in a hot springs-like soup warmer than most life can tolerate today.

The research, which will appear Thursday (Sept. 18) in the journal Nature, is expected to enliven a longstanding debate about the temperatures of Earth when life consisted only of microbes, long before the appearance of animals about a half billion years ago, the scientists say. The findings may help narrow the search for life on other planets.

Authors of the report include Drs. Eric Gaucher, postdoctoral associate at the University of Florida, Steven Benner, distinguished professor of chemistry at Florida, and J. Michael Thomson, postdoctoral fellow at the UNC School of Medicine’s department of cell and developmental biology who worked with Gaucher and Benner before moving to UNC.

"If you’re going to search for life on other planets, you can’t just randomly put a probe down and look for life," Gaucher said. "You want to land in a spot that you think is the most probable for hosting life. So having some idea of the temperature zone where you should put the probe will be helpful."

The Earth is believed to have formed about 4.5 billion years. For 700 million years, asteroids and other celestial bodies smacked and smashed the new planet in an era known as "the heavy bombardment." Much debate centers on when life first appeared, but some scientists believe the first evidence – consisting of chemical signatures of microbes found in ancient rocks – dates back to the end of the bombardment around 3.8 billion years ago, Gaucher said.

Earth’s climate from this period until the "Cambrian explosion" – the appearance of many forms of higher animals 570 million years ago – is thought to have varied widely through time. Evidence of glaciers at the equator suggests a "snowball Earth" much colder than today, while other evidence implies the planet went through comparatively warm periods, Gaucher said.

Geologists have dominated research on the topic, probing minerals and rocks in an effort to pen a timeline of Earth’s changing climate. The research team tried a different approach: recreating the ingredients of ancient life, and then testing their ability to persist and thrive in various temperatures.

Lynn Rothschild, a research scientist at NASA Ames Research Center and expert in astrobiology, said the approach was creative. "It is one of those clever pieces of work that makes me say, ‘I wish I’d thought of that,’" she said. "While this approach is not unique nor definitive, it provides a much-needed alternative approach to evolutionary studies."

The process sounds reminiscent of Jurassic Park, but there's a difference. Scientists in the popular Michael Crichton novel-turned-movies resurrect dinosaurs, which date back only about 60 million years. The team sought to go much further back -- at least a billion years.

They employed a technique called paleogenetics, first proposed in 1963 by famed scientists Linus Pauling and Emile Zuckerkandl. Technology then was not up to the authors’ dreams, but thanks to vast increases in the speed of information processing starting in the 1980s and other advancements in the laboratory, the concept became a reality late last decade.

The method is analogous to historical linguistics, which reconstructs ancient languages by finding similarities in their descendant languages. Instead of words or sounds, scientists match up similarities in the amino acids of various existing proteins to reconstruct the amino-acid sequences of ancient proteins. They then recreate, or "resurrect," these proteins in the laboratory.

Researchers started with 55 different modern bacteria, extracting a protein called "elongation factor tu," which is shared with other bacteria and most other modern organisms. They chose this bacteria in part because its prevalence suggests it appeared in a single or common ancestor and also because it is very stable, or doesn’t appear to have changed much over the eons.

The next step was to reconstruct the ancient protein. "We’re out at the end of the timeline, and we’re trying to go back," Gaucher said.

After sequencing each protein, the scientists used computer analyses to tease out the commonalities among those amino acid sequences. The result was a digital representation of the ancient protein. The next step was to resurrect it in the physical world. They used E. coli, a modern bacterium, to make the protein.

They then tested what happened to the protein at various temperatures. Between 130 and 150 degrees, it performed best at its task -- which involves translating the information in its DNA through RNA into the completed protein. At hotter temperatures, the ancient protein fell apart.

Benner cautioned the findings do not imply that the entire Earth was 130 to 150 degrees a billion years ago or longer, but rather that the bacterium whose genes survived to be relayed into descendant organisms thrived at that temperature. Why it proved so successful is a mystery, he said.

"For some reason, bacteria living at 130 to 150 degrees have made some innovation which allows them to leave their descendants all over the planet, not the other guys that we presume were living in other environments," he said. "And that’s an astonishment to me."

"We have now extended this research to understanding gene duplication events in the historical past by reconstructing the alcoholic fermentation pathway in yeast," said UNC’s Thomson. "Understanding why genes duplicate and are fixed in the genome may help scientists predict better model organisms to study."

He and his colleagues expect to publish their findings about the important fermentation process later this year or early next year.

The NASA Astrobiology Institute funded the continuing research.

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Note: Gaucher, Benner and Thomson can be reached at (352) 271-7005, (352) 392-7773 and (919) 966-3134, respectively.

UF Contact: Aaron Hoover, (352) 392-0186
UNC Contact: David Williamson, (919) 962-8596