Elucidating the Morphology of the Endoplasmic Reticulum: Puzzles and Perspectives

Artificial or synthetic organelles are a key challenge for bottom-up synthetic biology. So far, synthetic organelles have typically been based on spherical membrane compartments, used to spatially confine selected chemical reactions. In vivo, these compartments are often far from being spherical and can exhibit rather complex architectures. A particularly fascinating example is provided by the endoplasmic reticulum (ER), which extends throughout the whole cell by forming a continuous network of membrane nanotubes connected by three-way junctions. The nanotubes have a typical diameter of between 50 and 100 nm. In spite of much experimental progress, several fundamental aspects of the ER morphology remain elusive. A long-standing puzzle is the straight appearance of the tubules in the light microscope, which form irregular polygons with contact angles close to 120°. Another puzzling aspect is the nanoscopic shapes of the tubules and junctions, for which very different images have been obtained by electron microcopy and structured illumination microscopy. Furthermore, both the formation and maintenance of the reticular networks require GTP and GTP-hydrolyzing membrane proteins. In fact, the networks are destroyed by the fragmentation of nanotubes when the supply of GTP is interrupted. Here, it is argued that all of these puzzling observations are intimately related to each other and to the dimerization of two membrane proteins anchored to the same membrane. So far, the functional significance of this dimerization process remained elusive and, thus, seemed to waste a lot of GTP. However, this process can generate an effective membrane tension that stabilizes the irregular polygonal geometry of the reticular networks and prevents the fragmentation of their tubules, thereby maintaining the integrity of the ER. By incorporating the GTP-hydrolyzing membrane proteins into giant unilamellar vesicles, the effective membrane tension will become accessible to systematic experimental studies.

A Model of Lipid Monolayer-Bilayer Fusion of Lipid Droplets and Peroxisomes

Lipid droplets are unique organelles that store neutral lipids encapsulated by the lipid monolayer. In some processes of cellular metabolism, lipid droplets interact with peroxisomes resulting in the fusion of their envelopes and the formation of protrusions of the peroxisome monolayer, called pexopodia. The formation of pexopodia is facilitated by free fatty acids generated during lipolysis within lipid droplets. In this work, we studied the fusion of monolayer and bilayer membranes during the interaction between lipid droplets and peroxisomes. To this end, we built the energy trajectory of this process using the continuum elasticity theory and investigated the molecular details of the fusion structures utilizing molecular dynamics. We divided the fusion process into two stages: formation of a stalk and its consequent expansion into pexopodia. We found that in the considered system, the stalk was energetically more stable and had a lower energy barrier of formation compared to the case of bilayer fusion. The further evolution of the stalk depended on the value of the spontaneous curvature of the membrane in a threshold manner. We attributed the possible expansion of the stalk to the incorporation of free fatty acids into the stalk region. The developed model allowed describing quantitatively the process of monolayer-bilayer fusion.

Thermodynamics and In-Plane Viscoelasticity of Anionic Phospholipid Membranes Modulated by an Ionic Liquid

This article presents the effects of an imidazolium-based ionic liquid (IL) on the thermodynamics and in-plane viscoelastic properties of model membranes of anionic phospholipids. The negative Zeta potential of multilamellar vesicles of 14 carbon lipid 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) is observed to reduce due to the presence of few mole % of an IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF₄]). The effect was found to be stronger on enhancing the chain length of the lipid. The surface pressure-area isotherms of lipid monolayer formed at air-water interface are modified by the IL reducing the effective area per molecule. Further, the equilibrium elasticity of the film is altered depending upon the thermodynamic phase of the lipids. While the presence of the IL in the DMPG lipid makes it ordered in the gel phase by reducing the entropy, the effect is opposite in the fluid phase. The in-plane viscoelastic parameters of the lipid film is quantified by dilation rheology using the oscillatory barriers of a Langmuir trough. Even though the low chain lipid DMPG does not show any effect of IL on its storage and loss moduli, the longer chain lipids exhibit a prominent effect in the liquid extended (LE) phase. Further, the dynamic response of the lipid film is found to be distinctly different in the liquid condensed (LC) phase from that of the LE phase.

Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes

Cellular membranes self-assemble from and interact with various molecular species. Each molecule locally shapes the lipid bilayer, the soft elastic core of cellular membranes. The dynamic architecture of intracellular membrane systems is based on elastic transformations and lateral redistribution of these elementary shapes, driven by chemical and curvature stress gradients. The minimization of the total elastic stress by such redistribution composes the most basic, primordial mechanism of membrane curvature-composition coupling (CCC). Although CCC is generally considered in the context of dynamic compositional heterogeneity of cellular membrane systems, in this article we discuss a broader involvement of CCC in controlling membrane deformations. We focus specifically on the mesoscale membrane transformations in open, reservoir-governed systems, such as membrane budding, tubulation, and the emergence of highly curved sites of membrane fusion and fission. We reveal that the reshuffling of molecular shapes constitutes an independent deformation mode with complex rheological properties.This mode controls effective elasticity of local deformations as well as stationary elastic stress, thus emerging as a major regulator of intracellular membrane remodeling.

Mechanism of shaping membrane nanostructures of endoplasmic reticulum

A highly intricate architecture of endoplasmic reticulum (ER) membrane is crucial for the organelle functioning. Recent super-resolution microscopy studies discovered a nanoscopic level of ER organization characterized by 10- to 100-nm internal length scales. Deciphering the physical mechanisms of forming the ER nanostructures is a base for understanding the cell control of ER dynamics. Here, we proposed and computationally substantiated a common mechanism of shaping of all currently known ER nanostructures based on the intrinsic membrane curvature and ultra-low tensions as, respectively, a primary and a modulating factor.

Recent advances in super-resolution microscopy revealed the previously unknown nanoscopic level of organization of endoplasmic reticulum (ER), one of the most vital intracellular organelles. Membrane nanostructures of 10- to 100-nm intrinsic length scales, which include ER tubular matrices, ER sheet nanoholes, internal membranes of ER exit sites (ERES), and ER transport intermediates, were discovered and imaged in considerable detail, but the physical factors determining their unique geometrical features remained unknown. Here, we proposed and computationally substantiated a common concept for mechanisms of all ER nanostructures based on the membrane intrinsic curvature as a primary factor shaping the membrane and ultra-low membrane tensions as modulators of the membrane configurations. We computationally revealed a common structural motif underlying most of the nanostructures. We predicted the existence of a discrete series of equilibrium configurations of ER tubular matrices and recovered the one corresponding to the observations and favored by ultra-low tensions. We modeled the nanohole formation as resulting from a spontaneous collapse of elements of the ER tubular network adjacent to the ER sheet edge and calculated the nanohole dimensions. We proposed the ERES membrane to have a shape of a super flexible membrane bead chain, which acquires random walk configurations unless an ultra-low tension converts it into a straight conformation of a transport intermediate. The adequacy of the proposed concept is supported by a close qualitative and quantitative similarity between the predicted and observed configurations of all four ER nanostructures.

Membrane-Mediated Interactions Between Protein Inclusions

Integral or peripheral membrane proteins, or protein oligomers often get close to each other on cell membranes and carry out biological tasks in a collective manner. In addition to electrostatic and van der Waals interactions, those proteins also experience membrane-mediated interactions, which may be necessary for their functionality. The membrane-mediated interactions originate from perturbation of lipid membranes by the presence of protein inclusions, and have been the subject of intensive research in membrane biophysics. Here we review both theoretical and numerical studies of such interactions for membrane proteins and for nanoparticles bound to lipid membranes.

Remodeling of Membrane Shape and Topology by Curvature Elasticity and Membrane Tension

Cellular membranes exhibit a fascinating variety of different morphologies, which are continuously remodeled by transformations of membrane shape and topology. This remodeling is essential for important biological processes (cell division, intracellular vesicle trafficking, endocytosis) and can be elucidated in a systematic and quantitative manner using synthetic membrane systems. Here, recent insights obtained from such synthetic systems are reviewed, integrating experimental observations and molecular dynamics simulations with the theory of membrane elasticity. The study starts from the polymorphism of biomembranes as observed for giant vesicles by optical microscopy and small nanovesicles in simulations. This polymorphism reflects the unusual elasticity of fluid membranes and includes the formation of membrane necks or fluid 'worm holes'. The proliferation of membrane necks generates stable multi-spherical shapes, which can form tubules and tubular junctions. Membrane necks are also essential for the remodeling of membrane topology via membrane fission and fusion. Neck fission can be induced by fine-tuning of membrane curvature, which leads to the controlled division of giant vesicles, and by adhesion-induced membrane tension as observed for small nanovesicles. Challenges for future research include the interplay of curvature elasticity and membrane tension during membrane fusion and the localization of fission and fusion processes within intramembrane domains.

Using Atomic Force Microscopy To Illuminate the Biophysical Properties of Microbes

Since its invention in 1986, atomic force microscopy (AFM) has grown from a system designed for imaging inorganic surfaces to a tool used to probe the biophysical properties of living cells and tissues. AFM is a scanning probe technique and uses a pyramidal tip attached to a flexible cantilever to scan across a surface, producing a highly detailed image. While many research articles include AFM images, fewer include force-distance curves, from which several biophysical properties can be determined. In a single force-distance curve, the cantilever is lowered and raised from the surface, while the forces between the tip and the surface are monitored. Modern AFM has a wide variety of applications, but this review will focus on exploring the mechanobiology of microbes, which we believe is of particular interest to those studying biomaterials. We briefly discuss experimental design as well as different ways of extracting meaningful values related to cell surface elasticity, cell stiffness, and cell adhesion from force-distance curves. We also highlight both classic and recent experiments using AFM to illuminate microbial biophysical properties.

Influence of Platelet Lysate on 2D and 3D Amniotic Mesenchymal Stem Cell Cultures

The mechanobiological behavior of mesenchymal stem cells (MSCs) in two- (2D) or three-dimensional (3D) cultures relies on the formation of actin filaments which occur as stress fibers and depends on mitochondrial dynamics involving vimentin intermediate filaments. Here we investigate whether human platelet lysate (HPL), that can potentially replace fetal bovine serum for clinical-scale expansion of functional cells, can modulate the stress fiber formation, alter mitochondrial morphology, change membrane elasticity and modulate immune regulatory molecules IDO and GARP in amnion derived MSCs. We can provide evidence that culture supplementation with HPL led to a reduction of stress fiber formation in 2D cultured MSCs compared to a conventional growth medium (MSCGM). 3D MSC cultures, in contrast, showed decreased actin concentrations independent of HPL supplementation. When stress fibers were further segregated by their binding to focal adhesions, a reduction in ventral stress fibers was observed in response to HPL in 2D cultured MSCs, while the length of the individual ventral stress fibers increased. Dorsal stress fibers or transverse arcs were not affected. Interestingly, ventral stress fiber formation did not correlate with membrane elasticity. 2D cultured MSCs did not show differences in the Young's modulus when propagated in the presence of HPL and further cultivation to passage 3 also had no effect on membrane elasticity. In addition, HPL reduced the mitochondrial mass of 2D cultured MSCs while the mitochondrial mass in 3D cultured MSCs was low initially. When mitochondria were segregated into punctuate, rods and networks, a cultivation-induced increase in punctuate and network mitochondria was observed in 2D cultured MSCs of passage 3. Finally, mRNA and protein expression of the immunomodulatory molecule IDO relied on stimulation of 2D culture MSCs with pro-inflammatory cytokines IFN-γ and TNF-α with no effect upon HPL supplementation. GARP mRNA and surface expression was constitutively expressed and did not respond to HPL supplementation or stimulation with IFN-γ and TNF-α. In conclusion, we can say that MSCs cultivated in 2D and 3D are sensitive to medium supplementation with HPL with changes in actin filament formation, mitochondrial dynamics and membrane elasticity that can have an impact on the immunomodulatory function of MSCs.

Fundamental helical geometry consolidates the plant photosynthetic membrane

Plant photosynthetic (thylakoid) membranes are organized into complex networks that are differentiated into 2 distinct morphological and functional domains called grana and stroma lamellae. How the 2 domains join to form a continuous lamellar system has been the subject of numerous studies since the mid-1950s. Using different electron tomography techniques, we found that the grana and stroma lamellae are connected by an array of pitch-balanced right- and left-handed helical membrane surfaces of different radii and pitch. Consistent with theoretical predictions, this arrangement is shown to minimize the surface and bending energies of the membranes. Related configurations were proposed to be present in the rough endoplasmic reticulum and in dense nuclear matter phases theorized to exist in neutron star crusts, where the right- and left-handed helical elements differ only in their handedness. Pitch-balanced helical elements of alternating handedness may thus constitute a fundamental geometry for the efficient packing of connected layers or sheets.

Enhanced Protection of Biological Membranes during Lipid Peroxidation: Study of the Interactions between Flavonoid Loaded Mesoporous Silica Nanoparticles and Model Cell Membranes

Flavonoids, polyphenols with anti-oxidative activity have high potential as novel therapeutics for neurodegenerative disease, but their applicability is rendered by their poor water solubility and chemical instability under physiological conditions. In this study, this is overcome by delivering flavonoids to model cell membranes (unsaturated DOPC) using prepared and characterized biodegradable mesoporous silica nanoparticles, MSNs. Quercetin, myricetin and myricitrin have been investigated in order to determine the relationship between flavonoid structure and protective activity towards oxidative stress, i.e., lipid peroxidation induced by the addition of hydrogen peroxide and/or Cu²⁺ ions. Among investigated flavonoids, quercetin showed the most enhanced and prolonged protective anti-oxidative activity. The nanomechanical (Young modulus) measurement of the MSNs treated DOPC membranes during lipid peroxidation confirmed attenuated membrane damage. By applying a combination of experimental techniques (atomic force microscopy—AFM, force spectroscopy, electrophoretic light scattering—ES and dynamic light scattering—DLS), this work generated detailed knowledge about the effects of flavonoid loaded MSNs on the elasticity of model membranes, especially under oxidative stress conditions. Results from this study will pave the way towards the development of innovative and improved markers for oxidative stress-associated neurological disorders. In addition, the obtained could be extended to designing effective delivery systems of other high potential bioactive molecules with an aim to improve human health in general.

Cerium oxide nanoparticles at the nano-bio interface: size-dependent cellular uptake

The authors investigated the role of different size and morphology of cerium oxide nanoparticles (CNPs) in cellular uptake and internalization at the nano-bio interface. Atomic force microscopy (AFM) has been utilized to record changes in the membrane elasticity as a function of ceria particle morphology and concentration. Young's Modulus was estimated in presence and absence of CNPs of different sizes by gauging the membrane elasticity of CCL30 (squamous cell carcinoma) cells. Significant change in Young's Modulus was observed for CNP treatments at higher concentrations, while minimum membrane disruption was observed at lower concentrations. Studies using blocking agents specific to energy-dependent cellular internalization pathways indicated passive cellular uptake for smaller CNPs (3-5 nm). Other observations showed that larger CNPs were unable to permeate the cell membrane, which indicates an active uptake mechanism by the cell membrane. The ability of smaller CNPs (3-5 nm) to permeate the cell membrane without energy consumption by uptake pathways suggests potential for use as nanovectors for the delivery of bioactive molecules. Specifically, the passive uptake mechanism allows for the delivery of surface-bound molecules directly to the cytoplasm, avoiding the extreme chemical conditions of endosomal pathways.

The Use of Cell Elastography to Study the Biomechanical Properties of Bacillus subtilis

The cytometric, elastic, and adhesion properties of Bacillus subtilis at different terms of culturing were studied. The cytometric parameters of bacterial cells increased by day 6 in culture and decreased at later terms. Analysis of membrane rigidity showed that parameters describing bacterial elastic properties underwent waveform changes: the decrease in bacterial elasticity (from day 1 to 6) was followed by its increase on day 12 in culture. Analysis of adhesion activity showed that this parameter increased during the first 6 days and than decreased at later stages culturing.