With everything going green these days, it's unlikely that there's still much of a future in plastics, as Walter Brooke's Mr. McGuire famously advised Dustin Hoffmann's Benjamin in "The Graduate."
Synthetics, though, are another matter. Synthetic biology currently is reporting near-weekly progress in improving - or at least expanding - Mother Nature's repertoire.
Last month, researchers from the J. Craig Venter Institute reported that they had managed to transplant an entire bacterial genome from one bacterial species to another, a feat that co-author Craig Venter called a "huge enabling step" toward the creation of artificial life. (See BioWorld Today, June 29, 2007.)
Now, researchers from the Salk Institute in La Jolla, Calif., have added another tool to synthetic biology's kit: the ability to incorporate unnatural amino acids into mammalian cells.
The work, published in the July 2007 issue of Nature Neuroscience, is an extension of earlier studies in yeast and oocytes. (See BioWorld Today, April 25, 2001.)
Only 20 amino acids are used as building blocks by cells. But that's not for lack of the ability to use more. With four base pairs available, the genetic code provides no fewer than 64 different combinations of DNA triplets.
Three of those triplets are stop codons that signal the end of a protein. In their paper, the researchers described how they generated a tRNA synthetase that was able to recognize the stop codon TAG, also known as the amber stop codon. "In the presence of an amber suppressor tRNA, the amber codon will not signal stop, but be suppressed with the amino acid that is loaded on the amber suppressor tRNA," co-author Lei Wang, an assistant professor at the Salk Institute, explained to BioWorld Today.
One might expect that a t-RNA synthetase that reads through a stop codon is not the best thing for maintaining genetic law and order in a cell, but the amber tRNA synthetase did not appear to cause a deluge of overlong proteins. Wang said that rewiring a stop codon causes fewer problems than using another codon. Most codons code for an amino acid, and "if you change those codons, you would create a much worse situation in the cell."
He added that it is well known that many organisms can tolerate the suppression of stop codons quite well. As for why this is the case, Wang said that "currently we don't have a definitive answer," adding that his team is investigating possible reasons that the synthetic amino acid is not being incorporated at stop codons throughout the cell. Possible explanations include the fact that many proteins have several stop codons at their end, so if the first is suppressed, the protein simply is terminated at the second one. Another reason is that the suppression might not be very efficient. "If you got 100 percent suppression, it might be very toxic," Wang said.
The researchers made a synthetase that adds O-methyl-L-tyrosine, or Ome-Tyr, to the amino acid chain at the sites of TAG codons, which has a larger side chain than any naturally occurring amino acid.
In collaboration with neurobiologist Paul Slesinger and his group, Wang's lab used the method to study the characteristics of a potassium channel that helps to restore ion balance after a neuron fires.
"We first changed the tyrosine codon into the amber stop codon in the gene of the potassium channel. This mutant gene was introduced into mammalian cells together with genes for the new tRNA and synthetase," Wang said. Ome-Tyr then was added to the growth medium, taken up by the neurons and incorporated into the potassium channel.
The researchers found that Ome-Tyr's, bulky side chain greatly slowed down the channel's closing, which confirms structural studies that suggested the tyrosine usually controls the channel's closing speed by physically blocking the channel pore.
The scientists already had introduced mutations substituting other naturally occurring amino acids for the regular tyrosine, Wang said. But none of those amino acids was sufficiently large to measurably change the channel's characteristics. "We couldn't see a difference with natural amino acids."
Gene therapy with synthetic amino acids is probably not in the wings. But Wang believes that aside from the basic research questions that can be answered with them, artificial amino acids have promise for creating therapeutic proteins with improved medical characteristics, such as half-life or potency. He said that several companies are working on creating such improved therapeutic proteins. "You can think of a lot of things it could be useful for."