Mechanism of bacteria's internal time bomb discovered
31 July 2009
Researchers at VIB, the Flanders Institute for Biotechnology in Belgium, have determined the structure and operating mechanism of the proteins involved in the ‘internal time bomb’ of bacteria.
This clears the road for finding ways to set the clock on this internal time bomb and, hopefully, in the process developing a new class of antibiotics. The research is published in the July 31 issue of Molecular Cell .
For years, Nathalie De Jonge, Remy Loris and their colleagues of the VIB Department of Molecular and Cellular Interactions at Vrije Universiteit Brussel (VUB), have applied their relentless dedication to the study of the precise structure and function of the toxin-antitoxin complex, a system that had not been the focus of much interest in the past. Only in the last couple of years the rest of the scientific world come to realize its importance and as a result the number of papers in this field has exploded.
Bacteria have developed a handy way of providing extra protection from damage to important genes — the toxin-antitoxin (T-A) system. These T-A genes are tucked in near the genes to be protected. T-A genes contain instructions for both a toxin and its antitoxin.
As long as the cell is producing both, all is well. However, if for some reason the piece of DNA where the T-A gene is located gets damaged or lost, the production of toxin and antitoxin comes to a halt and a time bomb starts ticking.
Because the toxin is more stable than the antitoxin, it is broken down more slowly by the cell’s clean-up mechanisms. Once the antitoxin is all gone, there is still enough toxin left to kill the bacterium. The upshot for the species is that bacteria that lose their T-A gene — and probably have sustained damage to the important genes just next to it — can no longer reproduce.
Our best-known intestinal residents, Escherichia coli bacteria, more commonly known as E. coli, have such a T-A system in five different locations in their DNA, while Mycobacterium tuberculosis bacteria even have them in 60 locations.
A difficult feat
The T-A mechanism has been known for a while, but nobody clearly understood the workings of the proteins carrying out the instructions of the T-A gene. The VIB researchers clarified in detail both the appearance of the toxin and antitoxin, the mechanism of their interaction and the forms they take while in action — a difficult feat to pull off, requiring the simultaneous use of a whole range of different technologies. One of the difficulties for instance lay in the fact that part of the antitoxin lacks a fixed structure. This formlessness keeps it from being brought into view.
Now that we finally know how the time bomb functions (or more exactly, one of the time bombs, as there are several closely related T-A systems), biomedical scientists can start looking for substances to start the time bomb of pathogens ticking, ie substances that imitate the toxin protein, block the antitoxin protein, or disrupt the interaction between the toxin and antitoxin. In time, a new class of antibiotics might come out of it — though nature mostly has a countermove up its sleeve against any move scientists do.
VIB has a public enquiry email address for issues around this discovery:
1. De Jonge N., Garcia-Pino A., Buts L., Haesaerts S., Charlier D.,
Zangger K., Wyns L., De Greve H., Loris R. (2009) Rejuvenation of CcdB-poisoned
gyrase by an intrinsically disordered protein domain. Mol Cell (31 July
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