Expanding the Code: Engineered bacteria are genetic rebels

In an ongoing effort to push the limits of genetic engineering, researchers have created a bacterium that can incorporate artificial amino acids into its proteins and do so by breaking a fundamental rule of molecular biology.

Virtually all organisms build their life-sustaining proteins from a set of 20 amino acids, as encoded in an organism’s DNA. The genetic code is represented by sequences of four types of nucleotides, designated by the letters A, T, G, and C.

Those sequences are broken down into three-letter blocks called codons. The cell’s molecular machinery translates each codon into an amino acid and strings those amino acids together to form proteins.

To create an organism capable of making proteins from amino acids beyond the basic set of 20, a team of researchers led by Peter Schultz at the Scripps Research Institute in La Jolla, Calif., decided to expand the genetic code.

Instead of having a three-letter codon system, the researchers created a four-letter system.

That “opens the possibility of adding multiple unnatural amino acids to the genetic code,” says Christopher Anderson, one of the Scripps members who developed the organism.

Previously, the Schultz lab tricked bacteria and yeast cells into translating a naturally occurring three-letter nonsense codon—one that normally has no associated amino acid—within the cells’ genomes into one of several artificial amino acids (SN: 8/16/03, p. 102: Available to subscribers at Amending the Genetic Code: Yeast adds new amino acids to its proteins). Although that enabled the organisms to churn out proteins using one extra amino acid, moving beyond 21 amino acids in this way would require the addition of new, unique codons, says Anderson.

In this latest experiment, the researchers engineered the gene-to-protein translation machinery of Escherichia coli cells to recognize the four-letter genetic sequence AGGA and to assign the artificial amino acid l-homoglutamine to that codon. The researchers modified the genetic sequence for myoglobin, an oxygen-carrying protein, with an AGGA string and inserted the modified genes into E. coli. When a cell synthesized the protein encoded by the engineered sequence, it would include the artificial amino acid when instructed to do so by an AGGA codon. The researchers report their results in an upcoming Proceedings of the National Academy of Sciences.

Anderson says it might be possible to coerce these cells to make proteins including dozens of artificial amino acids, perhaps leading to novel drugs, industrial enzymes, and polymers with unique properties.

“This is really great work,” says Andrew Ellington at the University of Texas at Austin. However, he notes that there are ways of genetically encoding extra amino acids without using four-letter codons.

For instance, researchers can take advantage of the built-in redundancy in the genetic code. In some cases, up to six different codons will code for the same amino acid. Within that group of codons, some are rarer than others. Hijacking those that are rare and reprogramming them to encode a different amino acid is another way of expanding the genetic code, he suggests.

“One of the stories of the 21st century is going to be that of deprogramming our simplistic view of molecular biology,” says evolutionary biologist Stephen Freeland of the University of Maryland in Baltimore County.