UB Scientists Report Fast, Simple Method of Generating "Designer" RNA Catalysts for Proteomics

Artificial “Sugazyme” catalyzes synthesis of novel proteins with special features

University at Buffalo chemists have developed a remarkably simple and effective biotechnological method for synthesis of novel proteins using amino acids that do not occur in nature by using unique, programmable ribozymes (enzymes made of RNA, or ribonucleic acid) that they evolved in the lab.

The technology, described in the July issue of Nature Biotechnology, provides a potentially important new tool in the field of proteomics, where scientists are working to understand all of the proteins that have been identified through the human genome project.

A related technology was described in a paper published by the researchers in the June 19 issue of the Journal of the American Chemical Society.

The researchers, from the Department of Chemistry in the UB College of Arts and Sciences, are discussing a research and licensing agreement with a company interested in commercializing the technology, for which UB has filed patents.

According to the UB chemists, scientists have been interested in efficiently harnessing the ability to attach unnatural amino acids to proteins since the first demonstration that it could be done, in 1987. Existing methods for doing so have been too complicated and too expensive for routine use in the laboratory.

Named after lead researcher Hiroaki Suga, UB assistant professor of chemistry, the programmable “Sugazyme” provides an efficient and economic shortcut to attachment of tRNA to unnatural amino acids.

The UB method generates the first artificial ribozyme that performs two unique steps that lead to the generation of novel proteins.

First, the Sugazyme is programmed to recognize an engineered (i.e. unnatural) tRNA, as well as various unnatural amino acids. Second, it then operates as a chemical matchmaker, joining the two to create the aminoacylated tRNA, the essential molecule for linking the genetic

code to amino acids, triggering protein synthesis.

“Our system has the potential to provide a simple method for the preparation of such aminoacyl-tRNAs for researchers who want to expand the amino-acid repertoire for protein synthesis,” said Suga.

The advantage of using so-called unnatural or non-natural amino acids designed in the lab is that they can be tailored with special functions that are not available in natural amino acids and that will aid researchers working in proteomics.

“In the Nature Biotechnology paper, we demonstrate that we have evolved a ribozyme that has a programmable feature for recognition of any desired tRNAs and that it can charge non-natural amino acids on the specific tRNA,” explained Suga, co-author with Yoshitaka Bessho and David R.W. Hodgson, both post-doctoral fellows in the UB Department of Chemistry.

A related technology for engineering similar “designer catalysts” developed by the group and described in detail in the Journal of the American Chemical Society, consists of a few simple steps: The scientists immobilize the ribozyme on an inexpensive gel, pack the resin into a column, add the amino acid and tRNA and shake it for about half an hour.

“When the resin is washed off, what’s left is the aminoacyl-tRNA with the immobilized ribozyme,” said Suga. “The desired aminoacyl-tRNA can then be isolated. It’s a very durable and convenient system.”

In the lab, the UB researchers have demonstrated that the system also is economical and able to be reused numerous times.

Suga’s co-authors on the paper in the Journal of the American Chemical Society are Hiroshi Murakami, post-doctoral fellow and Neil J. Bonzagni, doctoral candidate, both in the UB Department of Chemistry.

The work was funded by the National Institutes of Health, the National Science Foundation and the Human Frontier Science Program.