Biologists at the U.S. Department of Energy’s Brookhaven National Laboratory and their collaborators have discovered an aberrant protein that’s deadly to bacteria. In a paper just published in the journal PLOS ONE, the scientists describe how this erroneously built protein mimics the action of aminoglycosides, a class of antibiotics. The newly discovered protein could serve as a model to help scientists unravel details of those drugs’ lethal effects on bacteria—and potentially point the way to future antibiotics.
“Identifying new targets in bacteria and alternative strategies to control bacterial growth is going to become increasingly important,” said Brookhaven biologist Paul Freimuth, who led the research. Bacteria have been developing resistance to many commonly used drugs, and many scientists and doctors have been concerned about the potential for large-scale outbreaks triggered by these antibiotic-resistant bacteria, he explained.
“What we’ve discovered is a long way from becoming a drug, but the first step is to understand the mechanism,” Freimuth said. “We’ve identified a single protein that mimics the effect of a complex mixture of aberrant proteins made when bacteria are treated with aminoglycosides. That gives us a way to study the mechanism that kills the bacterial cells. Then maybe a new family of inhibitors could be developed to do the same thing.”
Following an interesting branch
The Brookhaven scientists, who normally focus on energy-related research, weren’t thinking about human health when they began this project. They were using E. coli bacteria to study genes involved in building plant cell walls. That research could help scientists learn how to convert plant matter (biomass) into biofuels more efficiently.
But when they turned on expression of one particular plant gene, enabling the bacteria to make the protein, the cells stopped growing immediately.
“This protein had an acutely toxic effect on the cells. All the cells died within minutes of turning on expression of this gene,” Freimuth said.
Understanding the basis for this rapid inhibition of cell growth made an ideal research project for summer interns working in Freimuth’s lab.
“Interns could run experiments and see the effects within a single day,” he said. And maybe they could help figure out why a plant protein would cause such dramatic damage.
Misread code, unfolded proteins
“That’s when it really started to get interesting,” Freimuth said.
The group discovered that the toxic factor wasn’t a plant protein at all. It was a strand of amino acids, the building blocks of proteins, that made no sense.
This nonsense strand had been churned out by mistake when the bacteria’s ribosomes (the cells’ protein-making machinery) translated the letters that make up the genetic code “out of phase.” Instead of reading the code in chunks of three letters that code for a particular amino acid, the ribosome read only the second two letters of one chunk plus the first letter of the next triplet. That resulted in putting the wrong amino acids in place.
“It would be like reading a sentence starting at the middle of each word and joining it to the first half of the next word to produce a string of gibberish,” Freimuth said.
The gibberish protein reminded Freimuth of a class of antibiotics called aminoglycosides. These antibiotics force ribosomes to make similar “phasing” mistakes and other sorts of errors when building proteins. The result: all the bacteria’s ribosomes make gibberish proteins.
“If a bacterial cell has 50,000 ribosomes, each one churning out a different aberrant protein, does the toxic effect result from one specific aberrant protein or from a combination of many? This question emerged decades ago and had never been resolved,” Freimuth said.
The new research shows that just a single aberrant protein can be sufficie