Scientists Probing the Origins of Life Develop Method of Making Novel Proteins Using a 21st Amino Acid

BUFFALO, N.Y. -- Investigations into the origins of life and the genetic code have resulted in a method of developing novel proteins that has enormous potential for the biotechnology industry while providing some important clues to answering the question: "How did life begin?"

The research provides significant evidence for the existence of the so-called RNA world, believed to be the evolutionary stage that predates present biological systems.

It was published today (April 2, 2001) by scientists at the University at Buffalo and the University of Tokyo in EMBO Journal (Vol. 20, no. 7), publication of the European Molecular Biology Organization.

In evolving new sequences of an RNA catalyst, the authors also have developed an efficient method of creating novel proteins built out of not just the 20 amino acids found in nature, but out of additional, so-called non-natural amino acids designed in the lab.

The research demonstrates for the first time that a precursor to transfer RNA -- the genetic material that is responsible for synthesizing proteins -- could have acted as the catalyst for reactions that link transfer RNA (tRNA) to amino acids in a pre-biological era.

Aminoacylation, as that reaction is called, is the key step that spurs translation, or protein synthesis in cells, but scientists probing how genes first came to generate life as we know it have been puzzled about how that crucial step came to be taken, without a catalyst to trigger it.

"Using an in vitro version of Darwinian natural evolution, we have evolved this RNA catalyst, which provides evidence for support that RNA may well have served as the evolutionary vehicle necessary for the development of present-day, DNA-protein-based life forms," said Hiroaki Suga, Ph.D., lead author and assistant professor of chemistry in the College of Arts and Sciences at the University at Buffalo.

With applications ranging from proteomics to drug design and novel catalysis, the synthesis method described in the paper for attaching the transfer RNA to an unnatural amino acid using a ribozyme, an RNA enzyme, has the potential to provide scientists with a highly potent tool for engineering brand new proteins.

The system also has vast applications for the development of molecules with built-in tracers to help researchers precisely target specific proteins in living cells. The advantage is that since existing proteins are designed to "lock onto" only the 20 natural amino acids, an unnatural amino acid would act as a highly stable molecular tag, unlike current probes that tend to alter the structure or somehow destabilize any protein to which they are attached.

A patent application has been filed for select catalytic RNA molecules, a method of constructing them and a method for identifying aminoacylating molecules.

Ever since the discovery in 1987 that it was feasible to attach unnatural amino acids to proteins, scientists have wondered how that tantalizing possibility with its potential for engineering proteins with entirely new functions could be harnessed in an efficient, cost-effective manner.

"Unnatural amino acid mutagenesis is very complicated," said Suga. "The biggest stumbling block is synthesizing the unnatural amino acid and attaching it to transfer RNA."

According to Suga, attachment is physically very difficult because it involves efficiently and accurately attaching a tiny amino acid to a large macromolecule, tRNA.

"Our ribozyme can do it," Suga said.

Dubbed "Sugazyme" by the group, this ribozyme offers a more efficient method of attaching tRNA to unnatural amino acids by using new RNA sequences that Suga evolved in his lab to bind selectively amino acids and ligate to tRNA without having to use the very specialized and hard-to-engineer protein enzymes that nature uses.

Suga noted that the current paper describes their success with the process in vitro, a method that produces minute amounts of the aminoacyl-tRNA. However, in the near future, the researchers expect to have an in vivo method, using recombinant methods, capable of producing infinite amounts.

The work was funded by the National Institutes of Health.