Ancient Protein, Reconstructed By "Paleobiochemists," Suggests Hot World

September 17, 2003

GAINESVILLE, Fla. — A billion years ago, the 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.

So say two University of Florida scientists who have used the newly developed 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, set to appear 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 findings also may help narrow the search for life on other planets, said Eric Gaucher, a National Research Council fellow and post-doctoral associate at the University of Florida, who is the lead author of the paper.

“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.” There is much debate about 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.

The climate on Earth 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 also 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. Gaucher and Steven Benner, a UF distinguished professor of chemistry, 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 is indeed clever and 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-movie-series resurrect dinosaurs, which date back only about 60 million years. Gaucher and Benner sought to go much further back – at least 1 billion years.

The scientists used a technique called paleogenetics, first proposed in 1963 by famed scientists Linus Pauling and Emile Zuckerkandl. Technology at that time was not up to these 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.

Gaucher started with 55 different modern bacteria, extracting a protein called elongation factor tu, which is shared with other bacteria and most other modern organisms. He 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 noted.

He sequenced each protein and, using computer analysis, teased out the commonalities among these amino-acid sequences. The result was a digital representation of the ancient protein. The next step was to resurrect it in the physical world. Gaucher used E. coli, a modern bacterium, to make the protein.

He and Benner 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 cautions 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.”

The paper’s other authors are J. Michael Thomson and Michelle Burgan, both former students at UF. The research was funded by $100,000 grant from the NASA Astrobiology Institute.