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January 20, 2016

The clock is ticking: Self-activating protein stops growth of bacteria

During periods of nutrient deprivation or stress bacteria stop their growth. A driving force in this process may be Fic proteins, enzymes that modify target proteins. Researchers at the Biozentrum of the University of Basel have now elucidated their activation mechanism in molecular detail. In their study published in PNAS they describe for a specific class of Fic proteins a sophisticated regulatory mechanism and demonstrate that these proteins are molecular timers.

Left: The active site of the Fic protein is partially blocked by a helix (purple). Right: The enzyme is able to modify the helix and thereby overcome this blockage to activate itself.

In the cell they are usually inconspicuous. But once Fic proteins unfold their full action, the consequences are drastic: the cell ceases to grow. An interdisciplinary team of researchers from the Biozentrum, University of Basel, has carried out experiments in the test tube to study the regulation of the Fic protein from the meningococcus (meningitis pathogen) and have discovered two opposing mechanisms: While the silent ground state gets autonomously activated within a few minutes, active and potentially effective Fic proteins are immediately intercepted. Thus Fic proteins show a highly complex activity profile.

Fic proteins relief their blockage autonomously

Fic proteins are constantly being produced in the cell. At first they are inactive, since a helix of the protein is blocking the active site, similar to a lid covering a pot. Only when the lid is lifted, the enzyme becomes active. Then, the enzyme attaches adenosine monophosphate (AMP) to its target, a protein called gyrase. This leads to the inactivation of gyrase, which thus is no longer able to facilitate essential cellular processes such as the transcription and replication of DNA.

“For the first time we have been able to demonstrate that the self-blockage of the Fic protein is lifted by an entirely autonomous and time-dependent mechanism”, explains Frédéric Stanger, first author of the paper. “The lid is, in fact, not firmly placed on the pot but now and then lifts off. That’s when the enzyme can attach AMP to its own lid and thus irreversibly unblock the active site.” Furthermore, the research team discovered an opposing mechanism. Depending on the concentration, Fic proteins assemble to groups of four, which are again inactive. Both mechanisms together ensure that there is a pool of active Fic proteins that come into action only when they are needed.

Protein acts as a timer

Under adverse conditions, this dynamic and highly regulated system may become thrown out of balance. So, for instance, during starvation, when biosynthesis of proteins is turned down, the active form of Fic proteins will accumulate. As a result, the gyrases become inhibited and cell growth will come to a standstill. Due to the buffering capacity of the system, this effect will set in with a delay. “Physiologically, this delay, which we observed in the test tube, makes sense”, says Stanger. “It ensures that only under critical conditions cells stop growing and move into dormancy  to ensure that they can persist over a long time.” For the researchers, the next step will be to investigate the impact of this sophisticated regulatory mechanism within the living cell.

Original article:
Frédéric V. Stanger, Björn M. Burmann, Alexander Harms, Hugo Aragão, Adam Mazur, Timothy Sharpe, Christoph Dehio, Sebastian Hiller, and Tilman Schirmer. Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. Proceedings of the National Academy of Sciences PNAS, published online 19 January 2016.

Contact: Communications; Katrin Bühler