This nongenetic strategy always uses methionine, which can be oxidized without permanent damage, according to a paper in Nature.

When cells are confronted with an invading virus or bacteria or exposed to an irritating chemical, they protect themselves by inserting the wrong amino acid into new proteins to defend them against damage, scientists from the University of Chicago and NIAID have discovered. These “regulated errors” comprise a novel nongenetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed, say the scientists. The study was published November 26 in Nature.

“This mechanism allows every protein to get some protection,” says Tao Pan, professor of biochemistry and molecular biology at the university. “The genetic code is considered untouchable, but this is a nongenetic strategy used in cells to create a bodyguard for proteins.”

In artificial laboratory preparations, scientists have observed that only one out of every 10,000 amino acids is placed into a protein incorrectly, and thus protein errors were thought to be exceptionally rare. However, the researchers then observed how often tRNA errors, called misacylations, occurred in live cells. After developing a technique for measuring these errors, the authors were surprised to find a much higher error rate in those cells for the amino acid methionine. As high as one out of every 100 methionines was incorrectly placed in proteins, they found.

When the cells were stressed by exposure to a virus, bacteria, or a toxic chemical such as hydrogen peroxide, that error rate went even higher, as up to 10% of methionines placed into new proteins were different from what the gene specified. “That was 1,000 times more than the textbook says should be there,” Pan said.

Further experiments revealed that it was always the same amino acid, methionine, placed incorrectly into new proteins. Methionine is one of only two amino acids to carry sulfur atoms on its side chains, a feature that allows it to neutralize dangerous molecules called reactive oxygen species (ROS) that form inside an infected or stressed cell. ROS can damage proteins through oxidation, but methionine can be oxidized (and restored through reduction) without being permanently damaged.

“The idea is that methionine can protect you from having oxidation of the active site of protein, which would ultimately completely block function of the protein,” says Jeffrey Goodenbour, University of Chicago graduate student and co-lead author. “You end up reducing the total reactive oxygen species load in the cell. It’s a very interesting mechanism.”

Cells normally put methionines near important parts of a protein to protect those segments from being damaged by reactive oxygen species. When the cell is under stress, and the amount of ROS increases, the number of methionine “errors” is ramped up 10-fold, allowing new proteins to be even more resistant to attack.

“Think of a boxing match,” Pan says. “If you put methionine close to active site, the reactive oxygen species has to get past it to get to the active site residues for oxidization. You’ve put something right in front of it so a protein can take a hit. If you have a lot of methionines, to knock this protein out will take many, many hits. So this is a strategy used in cells to create a bodyguard for a protein.”

A remaining puzzle is to determine why extra protective methionines are not encoded as part of the DNA in the first place, instead of being left to the post-genetic random placement described in this paper. Pan suggests that random placement of the amino acids makes proteins even more resistant to attack, since no two are created alike.

“This sounds chaotic and doesn’t make a lot of sense according to the textbook,” Pan says. “But this way the cells can always ensure that a subset of these proteins is somewhat less sensitive to the extra hits. I think that’s the most important part of this—to make every protein molecule different—and you cannot do this genetically.”

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