Prof. Dr. Tilman Schirmer

Biozentrum
University of Basel
Klingelbergstrasse 50 / 70
CH - 4056 Basel
Biozentrum, Room 311 Phone: +41 61 267 20 89
Email: tilman.schirmer-at-unibas.ch
Curriculum Vitae

Administrative Assistant

Alexandra Eberhardt
Biozentrum, Room 308
Phone: +41 61 267 20 81
Email: alexandra.eberhardt-at-unibas.ch

Research group Tilman Schirmer

Molecular mechanisms of c-di-GMP signal transduction and AMP transferases

We are employing crystallographic and biochemical/ biophysical techniques to reveal the structural basis for the catalysis and regulation of c-di-GMP related proteins. Our second focus is on bacterial type IV secretion system (T4SS) effector proteins with AMP transferase activity.

Close of the EAL dimer of YahA (E. coli) induced by binding of c-di-GMP. Adopted from Sundriyal et al., 2014.

Make, break and recognition of c-di-GMP

Recent discoveries show that a novel second messenger, c-di-GMP, is extensively used by bacteria to control multicellular behavior, such as biofilm formation. Condensation of two GTP to the dinucleotide is catalyzed by GGDEF domains that usually occur in combination with sensory and/or regulatory modules. The opposing phosphodiesterase activity is provided by EAL domains that are similarly regulated.

In collaboration with the Jenal group (Biozentrum) and based on crystallographic and functional studies we have studied the catalytic and regulatory mechanisms of diguanylate cyclases, the enzymes that synthesize the second messenger. It appears that the general mechanism of activation relies on signal induced dimerisation of its regulatory domains that ensures productive of the two GTP loaded catalytic GGDEF domains. Currently, we are studying the molecular basis of phosphodiesterase regulation that are the antagonistic enzymes that degrade c-di-GMP. Although the active site is completely contained with their EAL domain, the domain is active only as a homodimer. This generic property of the catalytic domain is probably utilised in many of the full-length proteins to control their activity, very similar to the situation in diguanylate cyclades.

Thus our results provide clues about how this class of enzymes can be regulated in a modular and universal fashion by their sensory domains.

Recently we have started to elucidate the structures and binding modes of newly discovered c-di-GMP receptors. Furthermore, we are studying c-di-GMP regulated histidine kinases that thus provide a link between two-component and c-di-GMP signaling. The investigations will contribute to our knowledge of the complete c-di-GMP signal cascade.

Crystal structure of Fic protein VbhT in complex with anti-toxin VbhA (blue). Also shown is the ATP substrate (with electron density). Adopted from Engel et al., 2012.

Regulation of AMP transferases with FIC fold

Type IV secretion systems (T4SS) are utilized by many bacterial pathogens for the delivery of virulence proteins or protein-DNA complexes into their eukaryotic target cells. Together with the Dehio group (Biozentrum) we are working on a class of effector proteins that are composed of a FIC and a BID domain responsible for pathogenic action in the host cell (AMPylation of specific target proteins) and translocation, respectively.

Based on crystallographic analyses, we have found that FIC proteins are expressed in an inhibited form and are, thus, catalytically silent under normal circumstances. Inhibition is caused by partial obstruction of the ATP binding site by a helix that, depending on the Fic class, is provided by a cognate anti-toxin or is part of the enzyme itself. For the latter class, we are currently investigating the mechanism of auto-inhibition relief. Furthermore, we are interested in the structural basis of target recognition and, particular, target specificity. This knowledge may be utilized for drug development to target FIC proteins of bacterial pathogens.

KdgM porin folded to a small 12-stranded hollow β-barrel. Adopted from Hutter et al., 2014.

Porins

Porins are integral membrane proteins from the outer membrane of Gram-negative bacteria. They allow the uptake of nutrients by passive diffusion through an intrinsic pore that extends along the axis of the transmembrane β-barrel structure. After extensive work on the general trimeric porins OmpF and OmpC from E. coli, we have recently determined the high-resolution 12-stranded β-barrel structures of NanC from E. coli and KdgM from Dickeya dadantii, representatives of a porin family that is specific for the translocation of negatively charged poly-saccharides.