Thank the rare crested ibis for a clue that could one day help our bodies make better medicines.
The avian species is the only one known to naturally produce an enzyme capable of generating a noncanonical amino acid; that is, one that is not among the 20 required to encode most proteins.
That it exists – a discovery made by computationally comparing genomic databases – proves that this enzyme can work in the context of living cells, even if scientists don’t know what it’s doing for the bird.
But they have a pretty good idea of what it could do for us.
A new study by Rice University chemist Han Xiao, theoretical physicist Peter Wolynes and their colleagues shows that the amino acid sulfotyrosine (sTyr), a mutant of the standard amino acid tyrosine, is a key building block for programming living cells, which make therapeutic proteins express. It could potentially allow cells to serve as sensors, monitoring their environment and responding with the treatment needed.
To mimic the ibis’ ability to synthesize and incorporate sTyr into proteins, a cell’s DNA must be modified with a mutated codon, which in turn makes the avian transferase enzyme sulfotransferase 1C1. This catalyzes the formation of sTyr, an essential recognition component in a variety of biomolecular interactions.
The proof-of-concept study produced mammalian cells that synthesize sTyr for the first time. In one experiment, the Xiao lab made cells that boosted the effectiveness of thrombin inhibitors, anticoagulants used to prevent blood from clotting.
The study appears in nature communication.
In nature, most of our species are made up of 20 canonical building blocks. If you want to add an extra building block, you have to think about how to create it. We solved this problem: we can ask the cell to do it.
But then we must have the translation machinery to recognize it. And a special codon to encode this new building block. With this study, we have met all three of those requirements.”
Han Xiao, Rice University chemist
Xiao received a grant from the National Institutes of Health in 2019 to study whether cells can be programmed to make substances with extra amino acids. The new study shows the lab’s dramatic progress.
Until now, scientists have fed cells chemically synthesized non-canonical amino acids. Letting the cell do the work is far more efficient, Xiao said, but doing so will require the discovery of a new transferase enzyme with tyrosine pockets that could bind sulfate. This lock and key combination could then be used as the basis for a variety of catalytic converters.
“Through this new strategy for modifying proteins, we can now completely change the structure and function of a protein,” he said. “For our thrombin inhibitor models, we have shown that adding an unnatural building block to the drug can make the drug much more potent.”
It was worth a look to see if nature had knocked them down to a useful codon. Xiao hired Wolynes, co-director of the Center for Theoretical Biological Physics, whose lab compared genome databases and found sulfotransferase 1C1 in the ibis.
The Xiao lab used a mutant amber stop codon, a three-nucleotide group of uracil, adenine, and guanine, to encode the desired sulfotransferase, resulting in a fully autonomous mammalian cell line that can biosynthesize sTyr and convert it into proteins with great precision can install.
“We were lucky,” Xiao said. “Ibis is the only species that does this, which was discovered through a sequence similarity search of genomic information. After that, we asked if they could figure out why this enzyme recognizes tyrosine, but our human sulfotransferase doesn’t.”
The Wolynes team used AlphaFold2, an artificial intelligence program developed by Alphabet/Google’s DeepMind that predicts protein structures.
Researchers expect to use the combination of bioinformatics and computational screening to create a library of biosynthesized noncanonical amino acids.
Former Rice research assistant Yuda Chen, now a postdoctoral fellow at the University of California, San Francisco, and graduate student Shikai Jin are co-lead authors of the paper. Co-authors are graduate students Mengxi Zhang, Kuan-Lin Wu, and Yixian Wang; Student Anna Chung and postdocs Yu Hu, Shichao Wang and Zeru Tian.
Xiao is a Norman Hackerman-Welch Young Investigator and Assistant Professor of Chemistry, Bioengineering and Life Sciences and a CPRIT Fellow in Cancer Research. Wolynes is Professor of Natural Sciences at the DR Bullard-Welch Foundation and Professor of Chemistry, Life Sciences and Physics and Astronomy at Rice.
Cancer Prevention and Research Institute of Texas (RR170014), National Institutes of Health (R35-GM133706, R21-CA255894, and R01-AI165079), Robert A. Welch Foundation (C-1970), US Department of Defense (W81XWH – 21-1-0789), a John S. Dunn Foundation Collaborative Research Award, a Hamill Innovation Award, and the National Science Foundation-supported Center for Theoretical Biological Physics (2019745) supported the research.
Chen, Y. et al. (2022) Unlocking the potential of noncanonical amino acid biosynthesis to generate cells with precise tyrosine sulfation. nature communication. doi.org/10.1038/s41467-022-33111-4.