Filip Meersman

Rapid Acquisition of Gigapascal-High-Pressure Resistance by Escherichia coli

ABSTRACT Pressure and temperature are important environmental variables that influence living systems. However, while they vary over a considerable range on Earth and other planets, it has hardly been addressed how straightforwardly and to what extent cellular life can acquire resistance to extremes of these parameters within a defined genomic context and a limited number of generations. Nevertheless, this is a very pertinent question with respect to the penetration of life in allegedly inhospitable environments. In this study, directed evolution was used to reveal the potential of the nonsporulating and mesophilic model bacterium Escherichia coli to develop the ability to survive exposure to high temperature or pressure. While heat resistance could only marginally be increased, our data show that piezoresistance could readily and reproducibly be extended into the GPa range, thereby greatly exceeding the currently recognized maximum for growth or survival. IMPORTANCE While extremophilic microorganisms generally serve as the reference for microbial survival capacities in inhospitable environments, we set out to examine how readily a mesophilic model bacterium such as Escherichia coli could build up resistance to extremes of temperature or pressure within a very short evolutionary time scale. Both heat and high pressure constitute ecologically important physical stresses that are able to irrevocably penetrate the entire cell. Our results for the first time establish that cellular life can acquire resistance to pressures extending into the GPa range. While extremophilic microorganisms generally serve as the reference for microbial survival capacities in inhospitable environments, we set out to examine how readily a mesophilic model bacterium such as Escherichia coli could build up resistance to extremes of temperature or pressure within a very short evolutionary time scale. Both heat and high pressure constitute ecologically important physical stresses that are able to irrevocably penetrate the entire cell. Our results for the first time establish that cellular life can acquire resistance to pressures extending into the GPa range.

Nanomechanical and structural properties of native cellulose under compressive stress

Cellulose is an important biopolymer with applications ranging from its use as an additive in pharmaceutical products to the development of novel smart materials. This wide applicability arises in part from its interesting mechanical properties. Here we report on the use of high pressure X-ray diffraction and Raman spectroscopy in a diamond anvil cell to determine the bulk and local elastic moduli of native cellulose. The modulus values obtained are 20 GPa for the bulk modulus and 200-355 and 15 GPa for the crystalline parts and the overall elastic (Youngs) modulus, respectively. These values are consistent with those calculated from tensile measurements. Above 8 GPa, the packing of the cellulose chains within the fibers undergoes significant structural distortion, whereas the chains themselves remain largely unaffected by compression.

Structural and Mechanical Properties of TTR105-115 Amyloid Fibrils from Compression Experiments

Amyloid fibrils, originally associated with neurodegenerative diseases, are now recognized to have interesting mechanical properties. By using synchrotron x-ray diffraction at high pressure in a diamond anvil cell we determined the bulk modulus of TTR105-115 amyloid fibrils in water and in silicone oil to be 2.6 and 8.1 GPa, respectively. The compression characteristics of the fibrils are quite different in the two media, revealing the presence of cavities along the axis of the fibrils, but not between the β-sheets, which are separated by a dry interface as in a steric zipper motif. Our results emphasize the importance of peptide packing in determining the structural and mechanical properties of amyloid fibrils.

Unfolding and fibrillogenesis of insulin: Temperature, pressure and chemistry

Protein folding or unfolding can lead to the population of intermediates or partially unfolded conformations that have a high aggregation tendency. Some of these states associate in vivo to form fibrillar structures. These fibrils are the hallmark of molecular diseases such as Alzheimers disease. It has been suggested that in vitro fibril formation is a generic property of all proteins. Insulin has been chosen as a model protein to study the process of fibrillation with Fourier-transform infrared spectroscopy. It is found that the formation of fibrils is preceded by amorphous aggregation. We also investigated the effect of hydrostatic pressure on insulin fibrils. The observed spectral changes are interpreted in terms of fibril dissociation into protofilaments. Preliminary results indicate that pressure is an interesting tool to characterize the interactions that maintain the fibril structure.

Dynamics of the crystal to plastic crystal transition in the hydrogen bonded N-isopropylpropionamide

N-Isopropylpropionamide (NiPPA), which can self-associate via hydrogen bonds, was found to undergo a solid-solid transition as identified by DSC and X-ray diffraction. Below the melting temperature of 51 °C NIPPA adopts a plastic crystalline state with a tetragonal unit cell until it transforms into an ordered crystal with a monoclinic structure at temperatures ≤10 °C. Dielectric spectroscopy was used to characterize the dynamics of the system, determining the activation parameters for the plastic to crystalline phase transition. The activation enthalpy is relatively high, as expected for a system that involves hydrogen bonds. However, most of the activation energy as the plastic phase assumes a more crystalline state is due to the activation entropy, suggesting that the increased cooperativity observed in the relaxation processes is due to a steric locking of the molecules.

Phenoloxidase activity and thermostability of Cancer pagurus and Limulus polyphemus hemocyanin.

The intrinsic and inducible o-diphenoloxidase (o-diPO) activity of Cancer pagurus hemocyanin (CpH) and Limulus polyphemus hemocyanin (LpH) were studied using catechol, l-Dopa and dopamine as substrates. The kinetic analysis shows that dopamine is a more specific substrate for CpH than catechol and l-Dopa (K(m) value of 0.01 mM for dopamine versus 0.67 mM for catechol, and 2.14 mM for l-Dopa), while k(cat) is highest for catechol (2.44 min(-1) versus 0.67 min(-1) for l-Dopa and 0.71 min(-1) for dopamine). On treatment with 4mM sodium dodecyl sulfate (SDS) or by proteolysis the o-diPO activity of CpH increases about twofold. In contrast, native LpH shows no o-diPO activity, and exhibits only a slight activity after incubation with SDS. Neither CpH nor LpH show intrinsic mono-PO activity with l-tyrosine and tyramine as substrates. To explore the possible correlation between the degree of PO activity and protein stability of arthropod hemocyanins, the thermal stability of CpH and LpH was investigated by differential scanning calorimetry and Fourier transform infrared spectroscopy. CpH is found to be less thermostable (T(m)~80 °C), suggesting that the dicopper active sites are more accessible, thereby allowing the hemocyanin to show PO activity in the native state. The LpH, on the other hand, is more thermostable (T(m)~92 °C), suggesting the existence of a correlation between the thermal stability and the intrinsic PO activity of arthropod hemocyanins.

Reversible heat inactivation of copper sites precedes thermal unfolding of molluscan (Rapana thomasiana) hemocyanin

Hemocyanin (Hc) is a type-3 copper protein, containing dioxygen-binding active sites consisting of paired copper atoms. In the present study the thermal unfolding of the Hc from the marine mollusc Rapana thomasiana (RtH) has been investigated by combining differential scanning calorimetry, Fourier transform infrared (FTIR) and UV-vis absorption spectroscopy. Two important stages in the unfolding pathway of the Hc molecule were discerned. A first event, with nonmeasurable heat absorption, occurring around 60°C, lowers the binding of dioxygen to the type-3 copper groups. This pretransition is reversible and is ascribed to a slight change in the tertiary structure. In a second stage, with midpoint around 80°C, the protein irreversibly unfolds with a loss of secondary structure and formation of amorphous aggregates. Experiments with the monomeric structural subunits, RtH1 and RtH2, indicated that the heterogeneity in the process of thermal denaturation can be attributed to the presence of multiple 50kDa functional units with different stability. In accordance, the irreversible unfolding of a purified functional unit (RtH2-e) occurred at a single transition temperature. At slightly alkaline pH (Tris buffer) the C-terminal β-sheet rich domain of the functional unit starts to unfold before the α-helix-rich N-terminal (copper containing) domain, triggering the collapse of the global protein structure. Even around 90°C some secondary structure is preserved as shown by the FTIR spectra of all investigated samples, confirming the high thermostability of molluscan Hc.

Water dynamics in Shewanella oneidensis at ambient and high pressure using quasi-elastic neutron scattering

Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth’s deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7–1.1 Å−1 corresponding to real space dimensions of 6–9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.

From aggregation to chaperoning: Pressure effect on intermolecular interactions of proteins

The effect of pressure on the protein aggregation is shown in this paper. Deposition of insoluble protein aggregates is one of the key factors in the conformational diseases. Pressure counteracts the formation of intermolecular g -structure. Already slight pressurization to typically 2-3 kbar can destabilize aggregates of apo-horseradish peroxidase. On the other hand, the chaperone proteins, which prevent aggregation of damaged proteins exist in big oligomers. We show that pressure treatment of these aggregates changes the chaperone activity.

Laboratory investigation of high pressure survival in Shewanella oneidensis MR-1 into the gigapascal pressure range

The survival of Shewanella oneidensis MR-1 at up to 1500 MPa was investigated by laboratory studies involving exposure to high pressure followed by evaluation of survivors as the number (N) of colony forming units (CFU) that could be cultured following recovery to ambient conditions. Exposing the wild type (WT) bacteria to 250 MPa resulted in only a minor (0.7 log N units) drop in survival compared with the initial concentration of 108 cells/ml. Raising the pressure to above 500 MPa caused a large reduction in the number of viable cells observed following recovery to ambient pressure. Additional pressure increase caused a further decrease in survivability, with approximately 102 CFU/ml recorded following exposure to 1000 MPa (1 GPa) and 1.5 GPa. Pressurizing samples from colonies resuscitated from survivors that had been previously exposed to high pressure resulted in substantially greater survivor counts. Experiments were carried out to examine potential interactions between pressure and temperature variables in determining bacterial survival. One generation of survivors previously exposed to 1 GPa was compared with WT samples to investigate survival between 37 and 8°C. The results did not reveal any coupling between acquired high pressure resistance and temperature effects on growth.