Researchers at the University of North Carolina studied the catalytic properties of enzyme fragments, “protozymes,” and designer peptides to find evidence in support of the sense/antisense ancestry hypothesis for two enzyme superfamilies.
Researchers at the University of North Carolina studied the catalytic properties of enzyme fragments, “protozymes,” and designer peptides to find evidence in support of the sense/antisense ancestry hypothesis for two enzyme superfamilies.

Long before living cells evolved, there was the primordial soup, and it must have contained catalysts, but exactly how these relatively simple ingredients came to be remains unclear. Such catalysts likely included chemical species that developed the ability to accelerate an indispensable reaction—linking individual amino acids and adenosine triphosphate, or ATP, the energy-carrying molecule. This reaction is necessary to synthesize proteins and thus allow life to arise.

Creating links between amino acids and ATP is the specialty of two major enzyme superfamilies, Class I and Class II aminoacyl-tRNA synthetases. These superfamilies, say researchers at the University of North Carolina (UNC), may have developed from complementary chemical species that emerged at the dawn of life. Curiously, each superfamily may have arisen from the same piece of genetic code. That is, they may have been translated from opposite strands of the same ancestral gene.

The idea that a single gene, interpreted in two different ways, could account for two enzyme classes was first put forward by theoretical evolutionary biologists in 1994. Now this idea is supported by experimental evidence. This evidence was collected by a team of UNC scientists led by Charles Carter, Ph.D.

Dr. Carter's team devised experiments to physically take apart the synthetases to show that the necessary catalytic activity comes from parts of the enzymes that all members of each synthetase family share: the parts that bind to ATP. These parts—chains of 46 amino acids—compose about 5 to 10% of the total size of modern enzymes but exhibit more than 40% of their total activity.

Dr. Carter calls these enzyme fragments protozymes. His team found that the enzymatic activity of these protozymes focuses on the activation reaction with ATP.

This catalytic activity means that the protozymes were able to form very tight complexes with the least stable, slowest-to-form structures during the transitions that occur during the chemical reactions that form proteins. These tight complexes of enzymes within these “transition states,” Dr. Carter said, would be very necessary during catalysis and thus for the creation of the first life on Earth.

Dr. Carter then got help from UNC colleague Brian Kuhlman, Ph.D., to create “designer” protozymes from a single gene in which one strand codes for a protozymic ancestor of Class I synthetases and the other strand codes for a protozymic ancestor of Class II synthetases. (Class I synthetases activate half of the 20 amino acids that link togethery to form proteins, and Class II synthetases activate the other half.)

Surprisingly, their experiments revealed that both designer protozymes exhibited the same catalytic activity as did the protozymes Dr. Carter's team had isolated from the modern synthetases.

These results appeared June 18 in the Journal of Biological Chemistry, in an article entitled, “Functional Class I and II Amino Acid Activating Enzymes Can Be Coded by Opposite Strands of the Same Gene.”

This result unifies what scientists previously considered to be two distinct superfamilies of modern enzymes and greatly simplifies the complex process of forming the diversity of catalysts necessary for life: both catalysts were available at the same times and places before there were cells to package life's machinery.

“The activities of the two complementary peptides demonstrate that the unique information in a gene can have two functional interpretations, one from each complementary strand,” the authors wrote. “Further, designed 46mers achieve similar catalytic proficiency to wild-type 46mers by significant increases in both kcat and KM, supporting suggestions that the earliest peptide catalysts activated ATP for biosynthetic purposes.”

“We now have more information about how amino acids eventually evolved into complex molecules necessary to create life as we know it,” Dr. Carter explained. “But perhaps more importantly, we've been able to provide a new set of tools that will enable others to approach questions about the origin of life in ways that are scientifically sound and productive.”

And there are still questions about how all this happened.

“This doesn't yet solve the central chicken and the egg problem,” Dr. Carter pointed out. “Even the designed protozyme requires a ribosome to synthesize it and lead to protein creation. But what we've shown is that blueprints for life actually contained more information than anyone had realized because both strands of the ancestral gene were responsible for encoding the two classes of synthetases needed for the creation of proteins.”

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