Cellular toolkit opens up a world of possibilities

Cells are like novels: they’re made up of words and sentences, each spelled out in combinations of letters. All of cell biology is dictated by the letters of the genetic code, which determine the amino acid sequences of the proteins that carry out distinct tasks. Now, Yale scientists have shaken up the alphabet of life, adding a new letter to its mix.

“I really believe that the genetic code can evolve and expand,” says Dieter Söll, Ph.D., Sterling Professor of Molecular Biophysics and Biochemistry and professor of chemistry, senior author of a paper on the new work. “This is proof that we can make that happen.”

Genes are made up of four different nucleotides. Each triplet of nucleotides—called a codon—codes for one building block of a protein, called an amino acid. Since there are 64 possible DNA triplets in this genetic code, but only 22 standard amino acids, many codons are redundant.

Once a protein is assembled from a string of amino acids, other molecules can attach to these amino acids, altering the protein’s function. One example is phosphorylation, the addition of a phosphate molecule. When the amino acid serine is phosphorylated, the resulting compound is called phosphoserine. Many human diseases, including cancer, involve faulty phosphorylation, but it has been a struggle for scientists to find out more because they don’t know how cells add phosphate molecules in the first place.

“We don’t have tools that enable us to take a protein and phosphorylate certain serines in a controlled and precise way,” says Söll’s collaborator Jesse Rinehart, Ph.D., assistant professor of cellular and molecular physiology at the School of Medicine. “And that’s really limited our ability to study phosphorylation.”

Söll and Rinehart had an idea: what if they made a protein from scratch that had phosphoserine as one of the starting amino acids, rather than trying to add phosphate to serines later? “What we really wanted to do,” says Rinehart, “was to bypass the cell’s normal machinery, and produce proteins in a new way, using a new code.” The researchers didn’t want every serine to be a phosphoserine, but they wanted to mimic the pattern of phosphorylation found naturally in cells. Molecules called tRNA, the major research focus of Söll’s lab, match up codons with the appropriate amino acids. As described in the August 26 issue of Science, Rinehart and Söll created a new tRNA that matched phosphoserine to a rare codon that usually signals the end of a protein-coding message. “We made room for a new amino acid. This allows us to have control over where phosphoserine occurs,” says Rinehart.

Next, Söll and Rinehart engineered a mammalian gene that had the special codon in every place that they wanted a phosphoserine, then added the gene, the new tRNA, and some additional enzymes to a bacterial cell. The result: the bacterium churned out copies of the protein that had phosphoserine integrated into all the right spots.

Some proteins are activated by phosphorylation and others are shut off. By comparing proteins made with their new tool to those made with typical sequences, Söll and Rinehart will be able to precisely determine phosphorylation’s effects.

Phosphoserines aren’t the only modified amino acid, and Söll envisions using the new method to add phosphate and other molecules, such as acetyl and methyl groups, onto other amino acids. “There are lots of ways that we can expand this toolkit,” says Söll.

“You could say this is just a curiosity—we’ve done something that no one else has done before,” says Rinehart. “But in this case, it is more than that. There is a vast amount of medically important work that can be done now on phosphorylation.”