Biology subjects

Drace, T.

Publications and source records attributed to Drace, T..

4 recordsLinked to original sources

bioRxiv2025

Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms

Nucleocytoplasmic protein O-GlcNAcylation is an essential modification catalysed by O-GlcNAc transferase (OGT) and reversed by O-GlcNAc hydrolase (OGA), a multi-domain enzyme that also contains a C-terminal pseudo-histone acetyltransferase (pHAT) domain. OGA and OGT are tightly regulated using O-GlcNAc-dependent feedback mechanisms that are largely unknown. Although the structure of the OGA homodimeric catalytic domain has been reported, the structure and function of the pHAT domain remains poorly understood. We describe a crystal structure of the Trichoplax adhaerens pHAT domain and cryo-EM data of the multi-domain T. adhaerens and human OGAs, together with surface plasmon resonance and small-angle X-ray scattering studies. Our findings show that the eukaryotic OGA pHAT domains affect O-GlcNAc homeostasis, and form catalytically incompetent, symmetric homodimers, projecting a partially conserved putative peptide binding site available for interactions with binding partners. While there is evidence for symmetric OGA multi-domain dimers in solution, interactions between the linkers to the pHAT domains allow these to adopt a limited range of positions. In hOGA, the positions of the pHAT domains determine the wider active site environment through a key conformational change involving a tryptophan in a flexible arm region. Taken together, these multi-domain OGA structures reveal allosteric mechanisms of regulation.

molecular biology↗

bioRxiv2023

Comparative electric and ultrastructural studies of cable bacteria reveal new components of conduction machinery

Cable bacteria encompass at least two genera, and they are known to vary greatly in habitat preferences and filament thickness. We systematically investigated variations and similarities in cellular structures and electrical properties of different cable bacteria strains. Using SEM, TEM, STEM-EDX and ToF-SIMS, we characterized shared features of cable bacteria, such as inner and outer membranes, surface layer and cell junction architecture, as well as strain specific features, like the number and size of periplasmic conductive fibers (PCFs). Our data indicates that the PCFs are organized as loose stranded rope-like structures. With spatially resolved elemental analysis we detected nickel-containing co-factors within the PCF of cable bacteria strains in both genera suggesting a conserved conduction mechanism. Electrical conductivity of different cable bacteria strains showed a range of values covering three orders of magnitude indicating an unknown metabolic adaptation. Using cryogenic electron tomography we discovered multiple polar chemosensory arrays, abundant cytoplasmic inner membrane-attached vesicles (IMVs), polysomes and inner membrane invaginations that shed light on cable bacteria metabolism including complex motility control mechanisms, localized protein synthesis, and membrane remodeling. We propose that the IMVs discovered in this work are novel metabolic hubs closely connected to the unique conductive fiber structure of cable bacteria.

microbiology↗

bioRxiv2022

Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity

ABSTRACTMicrobially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Their critical role in rain formation and frost damage of crops together with their diverse commercial applications warrant an in-depth under-standing of their inherent ice nucleation mechanism. We used the machine-learning based software Al-phaFold to develop the first ab initio structural model of a bacterial INpro which is a novel beta-helix structure consisting of repeated stacks of two beta strands connected by two sharp turns. Using the synchrotron radiation circular dichroism, we validated the {beta}-strand content of the model. Combining functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity and the basis for investigating the mechanistic role of INpro-induced ice formation in the atmosphere, and for commercial design and production of ice-nucleating particles for industrial applications.

microbiology↗

bioRxiv2020

The Ice Nucleating Protein InaZ is Activated by Low Temperature

Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Utilizing specialized ice-nucleating proteins (INPros), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds and may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INPro-induced freezing have remained largely elusive. In the present study, we investigated the folding and the structural basis for interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae strain R10.79. Using vibrational sum-frequency generation and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a {beta}-helical structure in solution and at water surfaces. In this configuration, hydrogen bonding between INPros and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with spectral calculations and molecular-dynamics simulations shows that the INPro reorients at lower temperatures. We suggest that the reorientation can enhance order-inducing water interactions and, thereby, the effectiveness of ice nucleation by InaZ.

biophysics↗