Antibiotic molecules induce a dual effect on their molecular targets: while specifically binding to target molecules (a specific bacterial protein) and inhibiting its activity, they also induce an environmental response by the bacteria, eventually leading to genetically-driven resistance to these antibiotics. In turn, natural selection of these genetic alterations sometimes lead to gain of function and insensitivity to the antibiotic molecule. The question is, what is the mechanism by which an antibiotic molecule that inhibits DNA transcription, allows bacteria to keep living long enough to induce the environmental change leading to antibiotic resistance?
In acute conditions of Tuberculosis infection, antibiotics of the Rifamycin family are used for the specific inhibition of DNA transcription in bacteria. These antibiotic molecules bind with high affinity to one structure of the bacterial DNA transcription complex.
The transcription complex encompasses many different structures that are dynamically changing. Some of these structures allow transcriptional activity without the inhibition of Rifamycins. The problem is that these alternative dynamic structures are not abundant, and therefore were not yet characterized.
We characterize these dynamic structures using the combination of Single-molecule fluorescence spectroscopy, high information content mass-spectrometric techniques and computational simulations, with the aim: understanding the mechanisms of alternative transcriptional function in the presence of antibiotics. This will assist us in establishing the structural basis required for rational design of alternative antibiotics that will minimize the time window through which vacteria adapt, genetically change and develop resistance.