Scientists have used laboratory simulations to recreate conditions on early Earth and have discovered that the evolution of ancient proteins for all forms of life on the planet, including plants, animals and humans, would not have been possible without specific amino acids.
The discovery of the role that amino acids played in shaping the genetic code of ancient microorganisms sheds new light on the age-old mystery of the origin of life on Earth.
“You see the same amino acids in every organism, from humans to bacteria to archaea, and that’s because all things on Earth are connected through this tree of life that has an origin, an organism that was the ancestor of all living things,” Stephen said Fried, a Johns Hopkins chemist who led the research with researchers at Charles University in the Czech Republic. “We’re describing the events that shaped why that ancestor got the amino acids that it did.”
The results have recently been published in Journal of the American Chemical Society.
In the laboratory, the researchers mimicked primordial protein synthesis 4 billion years ago by using an alternative set of amino acids that were very abundant before life appeared on Earth.
They found ancient organic compounds integrated the amino acids best suited for protein folding into their biochemistry. In other words, life on Earth thrived not only because some amino acids were available and easy to make in ancient habitats, but because some of them were particularly good at helping proteins assume specific shapes to perform crucial functions.
“Protein folding basically allowed us to do evolution before there was even life on our planet,” Fried said. “You could have evolution before you had biology, you could have natural selection for the chemicals that are useful for life even before there was DNA.”
Although the original Earth had hundreds of amino acids, all living things use the same 20 of these compounds. Fried calls these connections “canonical.” But science has struggled to figure out what is so special—if anything—about these 20 amino acids.
In its first billion years, Earth’s atmosphere consisted of an assortment of gases such as ammonia and carbon dioxide that reacted with high levels of ultraviolet radiation to make some of the simpler canonical amino acids. Others arrived via the special delivery of meteorites, which introduced a mixed bag of ingredients that helped life on Earth complete a set of 10 “early” amino acids.
How the rest came to be is an open question that Fried’s team is trying to answer with the new research, especially since these space rocks brought much more than the “modern” amino acids.
“We’re trying to figure out what was so special about our canonical amino acids,” Fried said. “Were they chosen for a specific reason?”
Scientists estimate that the Earth is 4.6 billion years old, and that DNA, proteins and other molecules only began to form simple organisms 3.8 billion years ago. The new research provides new clues to the mystery of what happened in between.
“To have evolution in the Darwinian sense, you have to have this whole sophisticated way of flipping genetic molecules like DNA and RNA to proteins. But replicating DNA also requires proteins, so we have a chicken-and-egg problem,” Fried said. “Our research shows that nature could have selected building blocks with useful properties before Darwinian evolution.”
Scientists have seen amino acids in asteroids far from Earth, suggesting that these compounds are ubiquitous in other corners of the universe. Fried therefore believes that the new research may also have an impact on the possibility of finding life beyond Earth.
“The universe seems to love amino acids,” Fried said. “Maybe if we found life on another planet, it wouldn’t be so different.”
Reference: “Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability” by Mikhail Makarov, Alma C. Sanchez Rocha, Robin Krystufek, Ivan Cherepashuk, Volha Dzmitruk, Tatsiana Charnavets, Anneliese M. Faustino, Kosuke Leblike Fujishima, Stephen D. Fried and Klara Hlouchova, February 24, 2023, Journal of the American Chemical Society.
The study was funded by the Human Frontier Science Program and the NIH Director’s New Innovator Award.