Neutron scattering analysis of bacterial lipopolysaccharide phase structure. Changes at high pH

The aggregate structure of lipopolysaccharide isolated from an Re strain of Escherichia coli was examined at different pH values using small angle neutron scattering. At pH values of 6 and 7.4, angle-averaged scattering of the sodium salt of this isolate was consistent with randomly coiled tubular micelles approximately 100 A in diameter. At pH 9.1, however, Kratky analysis of the scattering data was distinctly different and consistent with pairing of uniform tubular micelle sections of length 1440 and 110 A in diameter. Contrast variation measurements of the micelles yielded an average micellar weight of the sample at pH 9.1 of approximately 1.11 X 10(7) daltons and suggested that the aggregates were tubular micelles of size and length similar to that derived from the scattering intensity data. Anisotropic scattering patterns of samples under shear indicated a rigidification of the micelles as the pH was increased to 9.1 and the temperature decreased from 25 to 10 degrees C. The rotational diffusion constants deduced from the observed shear anisotropy indicate that the structure at pH 9.1 must have smallest and largest dimensions which differ by at least an order of magnitude, ruling out spherical or moderately ellipsoidal structures. Analysis of the shear rate needed to induce anisotropic scattering indicated that the stiffness length of the micelles at pH 9.1 was approximately 1000 A and decreased at higher and lower pH values.     

Effect of high hydrostatic pressure on the bacterial mechanosensitive channel MscS

We have investigated the effect of high hydrostatic pressure on MscS, the bacterial mechanosensitive channel of small conductance. Pressure affected channel kinetics but not conductance. At negative pipette voltages (corresponding to membrane depolarization in the inside-out patch configuration used in our experiments) the channel exhibited a reversible reduction in activity with increasing hydrostatic pressure between 0 and 900 atm (90 MPa) at 23°C. The reduced activity was characterized by a significant reduction in the channel opening probability resulting from a shortening of the channel openings with increasing pressure. Thus high hydrostatic pressure generally favoured channel closing. Cooling the patch by approximately 10°C, intended to order the bilayer component of the patch by an amount similar to that caused by 50 MPa at 23°C, had relatively little effect. This implies that pressure does not affect channel kinetics via bilayer order. Accordingly we postulate that lateral compression of the bilayer, under high hydrostatic pressure, is responsible. These observations also have implications for our understanding of the adaptation of mechanosensitive channels in deep-sea bacteria.A Proceeding of the 28th Annual Meeting of the Australian Society for Biophysics.     

Substratum requirements for bacterial gliding motility

Flexibacter FS-1 filaments are unable to glide on agarose gels or on charge-neutralized glass unless those substrata are supplemented with the charged, cold water-soluble fraction of agar, or a variety of polyanionic polysaccharides derived from plants, yeasts and bacteria. Two graft polymers of xanthan gum also promote gliding motility under these conditions, as do an extracellular product of the bacteria themselves. A number of other polymers and small molecular species are ineffective as supplements. These results are considered in the context of the soil habitat of this Flexibacter. Among a variety of other gliding bacteria tested, several strains of the order Cytophagales also were unable to glide on agarose.Abbreviations CWSF Cold water-soluble fraction of agar - PMC 5 mM K phosphate buffer (pH 7)+0.1 mM MgCl₂+0.5 mM CaCl₂     

Experiments on ion channels at high pressure

Ion channels are distinctive membrane proteins which provide a gated pathway for diffusing ions. High pressure (<100 MPa) affects the kinetics of gating but not the conductance of the channel. Dynamic structural studies of channels at high pressure are, thus far, conspicuously absent but functional properties are studied at the single channel level with the patch clamp technique.     

Statistical measures of bacterial motility and chemotaxis

This paper presents a model for the three-dimensional microscopic behavior of motile bacteria, and relates its parameters to five practical measures of bacterial motility and chemotaxis (direction correlation function, diffusion constant, persistence time, average velocity, and up/down ratio). The attractant gradient dependences of persistence time, average velocity, and up/down ratio are related to a single function describing the gradient sensing mechanism.     

An improved sampling technique for bacterial cultures under high hydrostatic pressure

A sampling technique for bacterial cultures subjected to high hydrostatic pressure is described. A sample-receiving vessel with a motor driven interface-piston is employed. By precisely matching the pressures in the bulk culture and the sample-receiving vessel, none of the sample is subjected to the high shear forces common to other desings of high pressure sampler. The use of the technique was illustrated by the growth of an anaerobic culture at 300 bar and 75°C.     

A comprehensive genetic characterization of bacterial motility

We have developed a powerful experimental framework that combines competitive selection and microarray-based genetic footprinting to comprehensively reveal the genetic basis of bacterial behaviors. Application of this method to Escherichia coli motility identifies 95% of the known flagellar and chemotaxis genes, and reveals three dozen novel loci that, to varying degrees and through diverse mechanisms, affect motility. To probe the network context in which these genes function, we developed a method that uncovers genome-wide epistatic interactions through comprehensive analyses of double-mutant phenotypes. This allows us to place the novel genes within the context of signaling and regulatory networks, including the Rcs phosphorelay pathway and the cyclic di-GMP second-messenger system. This unifying framework enables sensitive and comprehensive genetic characterization of complex behaviors across the microbial biosphere.     

Footprinting of EcoRI endonuclease at high pressure.

Hydroxyl radicals generated by irradiation with gamma rays have been used to footprint EcoRI endonuclease with single base pair resolution at pressures up to 144 MPa. At atmospheric pressure (0.1 MPa) a 10 base pair footprint was found. With increasing pressure three types of responses were observed: (1) bases distant from the recognition sequence showed a moderate increase in solvent exposure; (2) the bases at the point of enzymatic activity showed a large increase in cleavage by the hydroxyl radicals; and (3) the two center-most bases exhibited no pressure-induced change in solvent accessibility. The results are interpreted in terms of localized conformational changes of EcoRI.     

Structure-based analysis of high pressure adaptation of alpha-actin

Deep-sea fishes occur to depths of several thousand meters, and at these abyssal depths encounter pressures that shallower living fishes cannot tolerate. Tolerance of abyssal pressures by deep-sea fish is likely to depend in part on adaptive modifications of proteins. However, the types of structural modifications to proteins that allow function at high pressure have not been discovered. To elucidate the mechanisms of protein adaptation to high pressure, we cloned the alpha-skeletal actin cDNAs from two abyssal Coryphaenoides species, C. armatus and C. yaquinae, and identified three amino acid substitutions, V54A or L67P, Q137K, and A155S, that distinguish these abyssal actins from orthologs of alpha-actin from non-abyssal Coryphaenoides. These substitutions, Q137K and A155S, prevent the dissociation reactions of ATP and Ca2+ from being influenced by high pressure. In particular, the lysine residue at position 137 results in a much smaller apparent volume change in the Ca2+ dissociation reaction. The V54A or L67P substitution reduces the volume change associated with actin polymerization and has a role in maintaining the DNase I activity of actin at high pressure. Together, these results indicate that a few amino acid substitutions in key functional positions can adaptively alter the pressure sensitivity of a protein.     

Chain length and oligonucleotide stability at high pressure

The effect of hydrostatic pressure on the helix-coil transition temperature (T_m) was measured for the DNA oligomers (dA)_n(dT)_n, where n = 11, 15, and 19, in 50 mM NaCl. The data were analyzed in light of previously published data for the polymer, poly(dA)·poly(dT) under the same conditions. As has been observed for DNA polymers, increasing the hydrostatic pressure led to an increase in the T_m of the oligomers; however, the effect of pressure diminished with decreasing chain length. The value of dT_m/dP decreased linearly with the inverse of the chain length varying from 3.15 × 10⁻²°C MPa⁻¹ for the polymer to 0.7 × 10⁻²°C MPa⁻¹ for the 11-mer. The two-state or van't Hoff enthalpy (ΔH_vH) of the helix-coil transition was obtained by analysis of the half-width of the thermal transition. As expected, ΔH_vH decreases with decreasing chain length. In contrast to the behavior of the polymer, poly(dA)·poly(dT), and (dA)₁₉(dT)₁₉, the ΔH_vH of the two shorter duplex oligonucleotides displayed a small pressure dependence dΔH_vH/dP≃−0.4 kJ MPa⁻¹ in both cases. The changes observed in the T_m and ΔH_vH were not sufficient to explain the magnitude of the chain-length dependence of the pressure effect. To interpret the large chain-length dependence of dT_m/dP, we propose that the terminal base pairs contribute a negative volume change to the helix-coil transition. Base pairs distant from the ends exhibit behavior characterized by the polymer where end effects are assumed to be negligible, i.e., a positive volume change for the helix-coil transition. The negative volume change of separating terminal bases may originate from the imperfect interactions these base pairs form with water due to the existence of several energetically equivalent conformations. This is reminiscent of one of the mechanisms proposed to be important in the pressure-induced dissociation of multimeric proteins into their constituent subunits. © 1996 John Wiley & Sons, Inc.     

Equilibrium shifts in enzyme reactions at high pressure

The effect of pressure on the equilibrium of a reaction was studied. Theoretical equilibrium constants and product concentrations have been calculated at elevated pressures. The theory is illustrated with an example of l-malate synthesis catalyzed by a fumarase. To study shifts in the equilibrium relatively low pressures can be applied (50–200 MPa), but our calculations show that for process optimisation much higher pressures (up to 1000 MPa) have to be used.

At these higher pressures, more stable enzymes are needed. We performed experiments with the hyperthermophilic β-glycosidase from Pyrococcus furiosus as a catalyst. Oligosaccharides were synthesized from glucose in an equilibrium reaction at pressures from 0.1 to 500 MPa. The enzyme remained active at 500 MPa. The equilibrium of the reaction was influenced by pressure and shifted towards the hydrolysis side, decreasing final oligosaccharide concentrations with increasing pressure. This pressure dependence of the final product concentration and the equilibrium constant could be described with a positive reaction volume of 2.4 mol/cm³.