Ancient Proteins

By comparing the DNA of related bacteria, scientists can catch a glimpse of Earth’s environment for life billions of years ago. How genes can take us back in time ? How genetics is providing a window to what the early Earth was like?

Each cell in an organism contains a DNA recipe book for the proteins the cell needs to operate. As species evolve, multiple versions of proteins appear. Cows and sheep might have a common ancestor — but now the digestive proteins in a cow are different from sheep proteins. This fact lets scientists look back into the past.

Steven Benner — a biochemist at the University of Florida — says it’s like knowing the German, English, and Russian words for snow. From those, you can reconstruct the ancient Indo-European word for snow.

Steven Benner: What it does is tell you that the Indo-European culture knew about snow which means they must have lived in a place where it did snow.

In 2002, Dr. Benner’s group compared DNA in modern bacteria. They reconstructed a genetic recipe for a protein possibly used a billion years ago. When they put a copy of the recipe into modern bacteria, the bacteria manufactured the ancient protein.

The team announced that the ancient protein worked best at 65 degrees Celsius — 150 degrees Fahrenheit — suggesting that early life on Earth thrived in a very warm environment.

Preliminary results of the work mentioned in today’s show was first announced at the American Geophysical Union [AGU] fall meeting in December 2002. It was at that meeting that Steven Benner gave the Union’s annual Carl Sagan Lecture. The researchers have since submitted papers on the topic, but the results have not yet been published as of this writing.

Researchers around the world are sequencing — that is, decoding — the genomes of hundreds of species. As more and more species’ DNA becomes available, researchers are able to work farther back in time. This type of research wouldn’t have been possible a few years ago! As more and more “cousins” become available for comparison, reconstructions will become more accurate. Reconstructing ancient proteins is a lot like reconstructing ancient languages.

Benner: “One thing that’s quite clear if you can look at sequences of proteins that are descended from any given ancestor, just like you reconstruct ancient languages from indo European languages by looking at the structure of langugaes that are derived from these languages, you can infer the structure of infer the structure these ancient proteins. If you look at French, Spanish, and Italian, you can make a guess what Latin looks like.”

Building the ancient proteins in the lab requires conning modern bacteria into manufacturing the ancient protein. Researchers place the genetic receipe for the ancient protein in the bacteria’s DNA.

Benner: “You can put that gene in a modern bacteria, you can get the modern bacteria to express that protein, and you can get something — you can some of that protein in your hands that was last seen naturally on on the earth 500 million years ago. “

Proteins are chains of amino acids that are coiled and doubled up into packages. The shape of the protein sometimes has an impact on how it performs its job inside the cell. Since heat often speeds up chemical reactions, it can make a protein’s job easier. But you have to strike a balance — if it gets too hot, the protein can unfold and fall apart. Too cold, and there are other problems with normal funcitioning. Somewhere there’s a sweet spot, a point where the protein does its job really well without being in danger of coming apart. That’s 65 degrees Celsius for this protein.

It is possible that different proteins would have different sweetspots. I think (although I can’t quite remember) that the researchers picked this protein because it assembles other proteins, so it’s pretty important that this protein work efficiently, since its a basic necessity for the cell.

Here’s more about early life forms. A lot of controversy swirls around the earliest life forms. Some more comments from Steven Benner…

Benner: “There’s been a large discussion of what kinds of forms primitive life has taken. Now almost everybody agrees that primitive life, that is life that lived more than 500 million years ago, was unicellular, it looked more like a bacterium than it looked like a human, for example. There is a general consensus about what core metabolism was, what kinds of proteins they had, how they synthesized new proteins, what kind of genetic code they had, many features of the biochemistry of the ancient organisms has been guessed at by these kinds of reconstructions. “

“One thing that has not been clear is what the physical environment of that microorganism was. This has been the subject of dozens of papers in the literature. Some people, thought it lived at very high temperatures, very high temperatures, some argued it lived at moderate or even cold temperatures. There are a variety of arguments that are adduced to try to make one case or the other.”

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