Ahmed Badran and Scripps Research colleagues have enhanced the synthetic biology toolkit in order to speed up investigations into gene expansion. Credit: Scripps Research
Modern biologists have a very ambitious goal: to understand how to modify or expand the genetic code of all life on Earth in order to create new life forms. This "synthetic biology research" is motivated by the desire to learn more about evolution and the logic behind the natural biology that we have inherited. There is also an important practical reason: Cells can be used to make a wide range of useful molecules, including protein-based therapeutics. These are responsible for an increasing number of new medicines. A cell that has a more extensive genetic code can make a wider range of medicines. This could greatly simplify the process of developing and manufacturing them.
It is still many years away from realizing the great goal of working, useful synthetic biology. Scientists have made a significant leap towards realizing the grand goal of a working, useful synthetic biology in this week's Nature Communications study, which has key components developed and demonstrated in an expanded genetic code system.
"We have added synthetic biology tools to speed up investigations into genetic code extension," said Ahmed Badran (study senior author, and assistant professor in Scripps Research's Department of Chemistry).
Cells use the natural genetic code that underlies life on Earth to translate information in DNA andRNA into amino-acid building blocks for proteins. The DNA and RNA molecules look like chains. They encode information using an alphabet of four nucleotide-building blocks or "letters". Transfer RNAs (tRNAs), which are molecular molecules, decode this information by recognising three letters at once and translating each "codon" into an amino-acid building blocks of a protein. Although this triplet codon system can encode 64 different amino acid (43) in principle, most organisms only use 20 amino acids.
The quadruplet system envisioned could, however, encode 256 (44) distinct amino acid. It is based on four-letter codens. Although most of these would not be found in natural proteins, some variations could exist on natural amino acids. This allows proteins to have more specific characteristics to maximize their effectiveness and safety, such as when used as medicines.
This is because the system of gene to protein translation is complex and requires multiple components to work well together. It took millions of years for the system we see in all living organisms on Earth to develop to its current efficiency and accuracy. Recent efforts to create whole new systems, such as quadruplet-codon, have shown promise.
In the new study, Badran and his team used an evolutionary, survival-of-the-fittest, technique called directed evolution to evolve a small set of tRNAs that in principle could work in a quadruplet system. These quadruplet-tRNAs can be used to translate sections of protein within bacterial cells, according to scientists. They were able translate six quadruplet codons consecutively, as well as four quadruplet codes in the same protein. This was at an efficiency that is not far from what would be required for a functional quadruplet.
Badran stresses that even though a quadruplet system code is still in its early stages of methods development, it could be very useful in enabling the simple synthesis protein with non-canonical amino acids, which aren't naturally found in proteins. These ncAAs could be used to give proteins new biological properties. They can also be used to attach toxic "warheads" to cancer drugs or to make chemical modifications to the protein.
"One could theoretically program a sequence of DNA that would be translated, in a living cell, into a protein that contains a complex set of modificationsmodifications that otherwise would be difficult or impossible to add," Badran says.
Badran joined Scripps Research in January and worked during the study at Harvard and the Broad Institute of MIT.
Badran was not the only co-author of the study "Multiplex suppression four quadruplet codons through tRNA directed evolution," which was also co-authored by Erika DelBenedictis, Gavriela Carrver, and Christina Chung, both of Yale University.
More information: Erika. A. DeBenedictis and colleagues, Multiplex suppression four quadruplet codons through tRNA-directed evolution, Nature Communications (2021). Information from Nature Communications Erika A. DeBenedictis and colleagues, Multiplex suppression for four quadruplet codons using tRNA-directed evolution, (2021). DOI: 10.1038/s41467-021-25948-y
