Gerhard Schenk | The University of Queensland, Australia (original) (raw)

Papers by Gerhard Schenk

Biochemical Journal, Jul 13, 2006

Bacterial phosphotriesterases are binuclear metalloproteins for which the catalytic mechanism has... more Bacterial phosphotriesterases are binuclear metalloproteins for which the catalytic mechanism has been studied with a variety of techniques, principally using active sites reconstituted in vitro from apoenzymes. Here, atomic absorption spectroscopy and anomalous X-ray scattering have been used to determine the identity of the metals incorporated into the active site in vivo. We have recombinantly expressed the phosphotriesterase from Agrobacterium radiobacter (OpdA) in Escherichia coli grown in medium supplemented with 1 mM CoCl 2 and in unsupplemented medium. Anomalous scattering data, collected from a single crystal at the Fe-K, Co-K and Zn-K edges, indicate that iron and cobalt are the primary constituents of the two metalbinding sites in the catalytic centre (α and β) in the protein expressed in E. coli grown in supplemented medium. Comparison with OpdA expressed in unsupplemented medium demonstrates that the cobalt present in the supplemented medium replaced zinc at the β-position of the active site, which results in an increase in the catalytic efficiency of the enzyme. These results suggest an essential role for iron in the catalytic mechanism of bacterial phosphotriesterases, and that these phosphotriesterases are natively heterobinuclear iron-zinc enzymes.

Microbiology Australia, Mar 6, 2023

The challenge of limiting global warming to below 1.5°C requires all industries to implement new ... more The challenge of limiting global warming to below 1.5°C requires all industries to implement new technologies and change practices immediately. The aviation industry contributes 2% of humaninduced CO 2 emissions and 12% of all transport emissions. Decarbonising the aviation industry, which relies heavily on high-density liquid fuels, has been difficult to achieve. The problems are compounded by the continued reliance on so-called sustainable aviation fuels, which use firstgeneration agricultural feedstocks, creating a trade-off between biomass for food and feed and its use as a feedstock for energy generation. Decarbonising aviation is also challenging because of problems in developing electric aircraft. Alternative feedstocks already exist that provide a more feasible path towards decelerating climate change. One such alternative is to use gas fermentation to convert greenhouse gases (e.g. from food production and food waste) into fuels using microbial acetogens. Acetogens are anaerobic microorganisms capable of producing alcohols from gaseous CO, CO 2 and H 2. Australia offers feedstock resources for gas fermentation with abundant H 2 and CO 2 production in proximity to each other. In this review, we put forward the principles, approaches and opportunities offered by gas fermentation technologies to replace our dependency on fossil fuels for aviation fuel production in Australia.

Journal of Inorganic Biochemistry, 2023

bioRxiv (Cold Spring Harbor Laboratory), Mar 25, 2020

Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to ano... more Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.

Chemistry: A European Journal, Nov 13, 2019

Chemistry: A European Journal, May 4, 2016

Current Topics in Biochemical Research, 2007

Frontiers in Chemistry

β-Lactams are the most widely employed antibiotics in clinical settings due to their broad effica... more β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn2+) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong...

Frontiers in Bioengineering and Biotechnology

In analogy to higher plants, eukaryotic microalgae are thought to be incapable of utilizing green... more In analogy to higher plants, eukaryotic microalgae are thought to be incapable of utilizing green light for growth, due to the “green gap” in the absorbance profiles of their photosynthetic pigments. This study demonstrates, that the marine chlorophyte Picochlorum sp. is able to grow efficiently under green light emitting diode (LED) illumination. Picochlorum sp. growth and pigment profiles under blue, red, green and white LED illumination (light intensity: 50–200 μmol m−2 s−1) in bottom-lightened shake flask cultures were evaluated. Green light-treated cultures showed a prolonged initial growth lag phase of one to 2 days, which was subsequently compensated to obtain comparable biomass yields to red and white light controls (approx. 0.8 gDW L−1). Interestingly, growth and final biomass yields of the green light-treated sample were higher than under blue light with equivalent illumination energies. Further, pigment analysis indicated, that during green light illumination, Picochlorum...

Scientific Reports, 2021

Aspergillus fumigatus is a fungal pathogen whose effects can be debilitating and potentially fata... more Aspergillus fumigatus is a fungal pathogen whose effects can be debilitating and potentially fatal in immunocompromised patients. Current drug treatment options for this infectious disease are limited to just a few choices (e.g. voriconazole and amphotericin B) and these themselves have limitations due to potentially adverse side effects. Furthermore, the likelihood of the development of resistance to these current drugs is ever present. Thus, new treatment options are needed for this infection. A new potential antifungal drug target is acetohydroxyacid synthase (AHAS; EC 2.2.1.6), the first enzyme in the branched chain amino acid biosynthesis pathway, and a target for many commercial herbicides. In this study, we have expressed, purified and characterised the catalytic subunit of AHAS from A. fumigatus and determined the inhibition constants for several known herbicides. The most potent of these, penoxsulam and metosulam, have Ki values of 1.8 ± 0.9 nM and 1.4 ± 0.2 nM, respectivel...

Antimicrobial Agents and Chemotherapy, 2021

The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active... more The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active-site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations were reported previously.

Nature, 2020

Materials and Methods Cloning, expression and purification of the AHAS subunits of S. cerevisiae ... more Materials and Methods Cloning, expression and purification of the AHAS subunits of S. cerevisiae in E. a b Supplementary Fig. 5. Comparison of negative staining electron micrographs of the AtAHAS and MtAHAS complexes. Left: AtAHAS complex. Right: MtAHAS complex. Both complexes have the characteristic Maltese cross shape observed in the X-ray structure of the fungal enzyme and in the cryo-EM image of the AtAHAS complex. These analyses were performed three times independently giving similar results. AtAHAS MtAHAS 40nm 40nm Supplementary Fig. 6. Images of the structure of the RSU dimer in the ScAHAS complex. a. The RSUs are divided into four regions: the N-terminal extension, the N-terminal domain, the Cterminal domain and the C-terminal extension (see Supplementary Fig. 2 for the sequence). ATP is shown as a red transparent surface and ball and stick model. b. Stereo view and zoom-in of the ACT domains of the RSU dimer. The ACT domains have a babbab sequence in their secondary structure.

Chemistry – A European Journal, 2020

This is the author manuscript accepted for publication and has undergone full peer review but has... more This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.

Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evol... more Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and deletion (“indel”) events, but available approaches exhibit limitations. To address these limitations, we developed Graphical Representation of Ancestral Sequence Predictions (GRASP), which efficiently implements maximum likelihood methods to enable the inference of ancestors of families with more than 10,000 members. GRASP implements partial order graphs (POGs) to represent and infer insertion and deletion events across ancestors, enabling the identification of building blocks for protein engineering.To validate the capacity to engineer novel proteins from realistic data, we predicted ancestor sequences across three distinct enzyme families: glucose-methanol-choline (GMC) oxidoreductases, cytochromes P450, and dihydroxy/sugar ac...