Aminoglycoside antibiotics such as kanamycin (Kan) bind to 16S rRNA in the A site of the 30S ribosomal subunit, interfering with the selection of cognate tRNAs during translation. Biologists at the U.S. Department of Energy’s Brookhaven National Laboratory led by Dr. Paul Freimuth have discovered an aberrant protein that’s deadly to bacteria. In a paper 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. 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.
The authors identified a single protein that mimics the effect of a complex mixture of aberrant proteins made when bacteria are treated with aminoglycosides. That gives them 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.
But when they turned on expression of one particular plant gene, enabling the bacteria to make the protein, the cells stopped growing immediately. The discovered protein had an acutely toxic effect on the cells. The authors found that all the cells died within minutes of turning on expression of this gene. 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.
The new research shows that just a single aberrant protein can be sufficient for the toxic effect. That wouldn’t be too farfetched. Nonsense strands of amino acids can’t fold up properly to become fully functional. Although misfolded proteins get produced in all cells by chance errors, they usually are detected and eliminated completely by “quality control” machinery in healthy cells. Breakdown of quality control systems could make aberrant proteins accumulate, causing disease. The next step was to find out if the aberrant plant protein could activate the bacterial cells’ quality control system or somehow block that system from working.
The research team found that the aberrant plant protein indeed activated the initial step in protein quality control, but that later stages of the process directly required for degradation of aberrant proteins were blocked. They also discovered that the difference between cell life and death was dependent on the rate at which the aberrant protein was produced. When cells contained many copies of the gene coding for the aberrant plant protein, the quality control machinery detected the protein but was unable to fully degrade it.
The authors findings indicated that the single aberrant plant protein killed cells by the same mechanism as the complex mixture of aberrant proteins induced by aminoglycoside antibiotics. But the precise mechanism of cell death is still a mystery. Scientists know that cells treated with the antibiotics become leaky, allowing things like salts to seep in at toxic levels. One hypothesis is that the misfolded proteins might form new channels in cellular membranes, or alternatively jam open the gates of existing channels, allowing diffusion of salts and other toxic substances across the cell membrane.
A next step would be to determine structures of our protein in complex with membrane channels, to investigate how the protein might inhibit normal channel function. That would help advance understanding of how the aberrant proteins induced by aminoglycoside antibiotics kill bacterial cells and could inform the design of new drugs to trigger the same or similar effects.
Mangala Tawde, Abdelaziz Bior, Michael Feiss, Feiyue Teng, Paul Freimuth. A polypeptide model for toxic aberrant proteins induced by aminoglycoside antibiotics. PLOS ONE. Published: April, 2022