We thank the rare crowned ibis for a clue that could one day help our bodies make better medicines.
The bird species is the only one known to naturally produce an enzyme capable of producing an illegal amino acid. That is, not one out of 20 is necessary for the coding of most proteins.
Its existence — a discovery made by computationally comparing genome databases — proves that it is possible for this enzyme to function in the context of living cells, even if scientists don’t know what it does to birds.
But they have a pretty good idea of what it can do for us.
A new study by Rice University chemist Han Xiao, theoretical physicist Peter Wolins and their colleagues shows that the amino acid, sulfotyrosine (sTyr), a mutant of the standard amino acid tyrosine, is an essential building block for programming living cells that express therapeutic proteins. It could allow cells to act as sensors that monitor their environments and respond with treatment.
Mimicking the ability of ibis to synthesize sTyr and incorporate it into proteins requires modification of the cell’s DNA with a mutated codon, which in turn makes the transferase enzyme, sulfotransferase 1C1, which is present in the bird. This stimulates the generation of sTyr, an essential part for recognizing a variety of biomolecular interactions.
A proof-of-concept study produced for the first time mammalian cells that make sTyr. In one experiment, Xiao’s lab made cells that boost the effectiveness of thrombin inhibitors, the anticoagulant used to prevent blood clots from forming.
The study appears in Nature Communications.
“In nature, most of our species is made up of 20 basic building blocks,” Xiao said. “If you want to add an extra building block, you have to think about how to make it. We solved this problem: we can ask the hive to make it.
“But then we have to have the translation mechanism to recognize it. And a special codon to encode this new building block,” he said. “Through this study, we met all three of these requirements.”
Xiao received a grant from the National Institutes of Health in 2019 to see if cells could be programmed to make substances containing additional amino acids. The new study demonstrates the lab’s exciting progress.
Until now, scientists had been introducing chemically synthesized non-canonical amino acids into cells. Getting the cell to do the work is much more efficient, Xiao said, but this requires discovering a new transferase enzyme with tyrosine pockets that can bind sulfate. This lock and key combination can then be used as the basis for a variety of triggers.
“Now, with this new strategy to modify proteins, we can completely change the structure and function of the protein,” he said. “For our models of thrombin inhibitors, we have shown that putting an abnormal building block into the drug can make the drug more effective.”
It was worth a look to see if nature beat them to a useful codon. For this, Xiao recruited Woolins, co-director of the Center for Theoretical Biophysics, whose lab compared genome databases and found 1C1 sulfotransferase in ibis.
Xiao’s lab used a mutated amber stop codon, a three-nucleotide group of uracil, adenine and guanine, to encode a required sulfotransferase, resulting in a completely independent mammalian cell line capable of biosynthesis of sTyr and incorporating it with great precision into proteins.
“We got lucky,” Xiao said. “Ibis is the only species that does this, which was discovered through a sequence similarity search for genomic information. Next, we asked if they could figure out why this enzyme recognizes tyrosine while our human sulfotransferase does not.”
Wolynes’ team used AlphaFold2, an artificial intelligence program developed by Google’s Alphabet/DeepMind that predicts the structures of proteins.
The researchers expect to use a combination of bioinformatics and computational enhanced screening to produce a library of biosynthetic non-canonical amino acids.
Former Rice Research Associate Yoda Chen, now a postdoctoral researcher at the University of California, San Francisco, and graduate student Shikai Jin are lead authors of the paper. Co-authors are graduate students Mengxi Zhang, Kuan-Lin Wu, and Yixian Wang; Undergraduate Anna Chong, and postdoctoral researchers Yu Hu, Wang Zhichao, and Tian Ziru.
Xiao is the young researcher Norman Hackerman-Welch and Assistant Professor of Chemistry, Bioengineering and Biosciences, and a CPRIT Investigator in Cancer Research. Wolins is Professor of Science at the Dr. Pollard Welch Foundation and Professor of Chemistry, Biosciences, Physics, and Astronomy at Rice.
The Cancer Prevention and Research Institute of Texas (RR170014), the National Institutes of Health (R35-GM133706, R21-CA255894 and R01-AI165079), the Robert A. Welch Foundation (C-1970), the US Department of Defense (W81XWH)-21-1-0789 ), the John S. Dunn Foundation Award for Collaborative Research, the Hamill Innovation Award, and Support for the Center for Theoretical Biophysics (2019745) supported by the National Science Foundation.