Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF).

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure-and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis, using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (ΔfadN) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA-fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n16:0 to a15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

Implementation of a self-consistent slab model of bilayer structure in the SasView suite.

Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. The use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.

Molecular origins of bulk viscosity in liquid water.

The rapid equilibrium fluctuations of water molecules are intimately connected to the rheological response; molecular motions resetting the local structure and stresses seen as flow and volume changes. In the case of water or hydrogen bonding liquids generally, the relationship is a non-trivial consideration due to strong directional interactions complicating theoretical models and necessitating clear observation of the timescale and nautre of the associated equilibrium motions. Recent work has illustrated a coincidence of timescales for short range sub-picosecond motions and the implied timescale for the shear viscosity response in liquid water. Here, neutron and light scattering methods are used to experimentally illustrate the timescale of bulk viscosity and provide a description of the associated molecular relaxation. Brillouin scattering has been used to establish the timescale of bulk viscosity; and borrowing the Maxwell approach, the ratio of the bulk viscosity, ζ, to the bulk modulus, K, yields a relaxation time, τB, which emerges on the order of 1-2 ps in the 280 K to 303 K temperature range. Inelastic neutron scattering is subsequently used to describe the motions of water and heavy water at the molecular scale, providing both coherent and incoherent scattering data. A rotational (alternatively described as localized) motion of water protons on the 1-2 ps timescale is apparent in the incoherent scattering spectra of water, while the coherent spectra from D2O on the length scale of the first sharp diffraction peak, describing the microscopic density fluctuations of water, confirms the relaxation of water structure at a comparable timescale of 1-2 ps. The coincidence of these three timescales provides a mechanistic description of the bulk viscous response, with the local structure resetting due to rotational/localized motions on the order of 1-2 ps, approximately three times slower than the relaxations associated with shear viscosity. In this way we show that the shear viscous response is most closely associated with changes in water network connectivity, while the bulk viscous response is associated with local density fluctuations.