UT researchers engineer bacteria to produce more-stable therapeutics

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A team of UT scientists recently perfected their method of using E. coli to produce more stable versions of therapeutic proteins by making the bacteria healthier. The method was published in the academic journal Nature Biotechnology on June 4, and is already being used to help create therapeutic medicines.

When making proteins, cells read their DNA’s code in groups of three called “codons,” which the cell then translates into the amino acids that make up proteins. In 2015, a collaboration between several UT labs, including Ross Thyer, Andrew Ellington, Raghav Shroff, Dustin Klein, Simon d'Oelsnitz, Victoria Cotham, Michelle Byrom and Jennifer Brodbelt published a method of replacing a codon in E. coli with a new amino acid that cells don’t naturally make, research associate Thyer said.

“Back in 2015 … we showed off the initial technology, which is recoding (a codon) as selenocysteine,” Thyer said. “And that worked in E. coli.”

Selenocysteine is identical to a normal amino acid called cysteine, except that selenocysteine has a selenium atom instead of a sulfur atom.

Scientists have long replaced sulfur with selenium in small medicinal proteins, allowing them to make stabler bonds, but this was done artificially in a lab, Thyer said. Using bacteria to produce larger, more complicated therapeutic proteins with selenocysteine already in them, Thyer said, is more efficient than individually making each molecule using lab instruments.

“A lot of proteins in the blood serum contain free cysteine(s that aren’t bonded to anything), and these can (bond) with the cysteines (in the therapeutic proteins) and mix them up,” Thyer said.

Additionally, the human body can be a “reducing environment,” meaning that many molecules can break cysteine’s sulfur bonds with electrons.

“(Selenium) bonds are resistant to both of these forms of bond breakage,” Thyer said.

When the team first developed a strain of E. coli that could make selenocysteine in 2015, the strain had many growth defects that made it unhealthy, Thyer said. Some of this was because the strain was engineered to remove a codon, but part of the problem was that the cells recognized the selenocysteine as toxic and would attempt to get rid of it.

Their new study showed that the strain could be made much healthier by “addicting” the E. coli to selenocysteine to ensure that the cells would not get rid of it.

“We started with the sickly strain, where selenocysteine was hampering the growth of the E. coli, and then we evolved that over a long amount of time,” said Shroff, a cell and molecular biology graduate student. “And we ended up with a strain that was officially able to incorporate selenocysteine, to the point that it was no longer toxic to the E. coli strain.”

The team also invented a protein that glows when exposed to selenocysteine and proved that their E. coli could make important therapeutic proteins and antibodies with the selenocysteine.

“We compared the proteins produced in each strain, one that contains the cysteines and one that contains the selenocysteines,” Thyer said.

The team’s modified strain produced proteins that lasted significantly longer in the human body. A pharmaceutical company, GRO Biosciences, is already using the new method.

“That strain … has been licensed out from UT to a startup Biotech company,” Thyer said. “And they are using it to produce therapeutics.”