Insights into autoregulation of a membrane protein complex by its cytoplasmic domains

Membrane transporters mediate the passage of molecules across membranes and are essential for cellular function. While the transmembrane region of these proteins is responsible for substrate transport, often the cytoplasmic regions are required for modulating their activity. However, it can be difficult to obtain atomic-resolution descriptions of these autoregulatory domains by classical structural biology techniques, especially if they lack a single, defined structure. The betaine permease, BetP, a homotrimer, is a prominent and well-studied example of a membrane protein whose autoregulation depends on cytoplasmic N- and C-terminal segments. These domains sense and transduce changes in K+ concentration and in lipid bilayer properties caused by osmotic stress. However, structural data for these terminal domains is incomplete, which hinders a clear description of the molecular mechanism of autoregulation. Here we used microsecond-scale molecular simulations of the BetP trimer to compare reported conformations of the 45-amino-acid long C-terminal tails. The simulations provide support for the idea that the conformation derived from electron microscopy (EM) data represents a more stable global orientation of the C-terminal segment under downregulating conditions while also providing a detailed molecular description of its dynamics and highlighting specific interactions with lipids, ions, and neighboring transporter subunits. A missing piece of the molecular puzzle is the N-terminal segment, whose dynamic nature has prevented structural characterization. Using Rosetta to generate ensembles of de novo conformations in the context of the EM-derived structure robustly identifies two features of the N-terminal tail, namely 1) short helical elements and 2) an orientation that would confine potential interactions to the protomer in the counterclockwise direction (viewed from the cytoplasm). Since each C-terminal tail only contacts the protomer in the clockwise direction, these results indicate an intricate interplay between the three protomers of BetP in the downregulated protein and a multidirectionality that may facilitate autoregulation of transport.

Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter

Tripartite ATP-independent periplasmic (TRAP) transporters are found widely in bacteria and archaea and consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains). HiSiaPQM and its homologs are TRAP transporters for sialic acid and are essential for host colonization by pathogenic bacteria. Here, we reconstitute HiSiaQM into lipid nanodiscs and use cryo-EM to reveal the structure of a TRAP transporter. It is composed of 16 transmembrane helices that are unexpectedly structurally related to multimeric elevator-type transporters. The idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. A model of the tripartite PQM complex is experimentally validated and reveals the coupling of the substrate-binding protein to the transporter domains. We use single-molecule total internal reflection fluorescence (TIRF) microscopy in solid-supported lipid bilayers and surface plasmon resonance to study the formation of the tripartite complex and to investigate the impact of interface mutants. Furthermore, we characterize high-affinity single variable domains on heavy chain (VHH) antibodies that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake, providing insight into how TRAP transporter function might be inhibited in vivo.

Arginine-rich cell-penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore

Arginine-rich cell-penetrating peptides do not enter cells by directly passing through a lipid membrane; they instead passively enter vesicles and live cells by inducing membrane multilamellarity and fusion. The molecular picture of this penetration mode, which differs qualitatively from the previously proposed direct mechanism, is provided by molecular dynamics simulations. The kinetics of vesicle agglomeration and fusion by an iconic cell-penetrating peptide-nonaarginine-are documented via real-time fluorescence techniques, while the induction of multilamellar phases in vesicles and live cells is demonstrated by a combination of electron and fluorescence microscopies. This concert of experiments and simulations reveals that the identified passive cell penetration mechanism bears analogy to vesicle fusion induced by calcium ions, indicating that the two processes may share a common mechanistic origin.

Arginine-rich cell-penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore

Arginine-rich cell-penetrating peptides do not enter cells by directly passing through a lipid membrane; they instead passively enter vesicles and live cells by inducing membrane multilamellarity and fusion. The molecular picture of this penetration mode, which differs qualitatively from the previously proposed direct mechanism, is provided by molecular dynamics simulations. The kinetics of vesicle agglomeration and fusion by an iconic cell-penetrating peptide-nonaarginine-are documented via real-time fluorescence techniques, while the induction of multilamellar phases in vesicles and live cells is demonstrated by a combination of electron and fluorescence microscopies. This concert of experiments and simulations reveals that the identified passive cell penetration mechanism bears analogy to vesicle fusion induced by calcium ions, indicating that the two processes may share a common mechanistic origin.

A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans

Based on serial sectioning, focused ion beam scanning electron microscopy (FIB/SEM), and electron tomography, we depict in detail the highly unusual anatomy of the marine hyperthermophilic crenarchaeon, Ignicoccus hospitalis. Our data support a complex and dynamic endomembrane system consisting of cytoplasmic protrusions, and with secretory function. Moreover, we reveal that the cytoplasm of the putative archaeal ectoparasite Nanoarchaeum equitans can get in direct contact with this endomembrane system, complementing and explaining recent proteomic, transcriptomic and metabolomic data on this inter-archaeal relationship. In addition, we identified a matrix of filamentous structures and/or tethers in the voluminous inter-membrane compartment (IMC) of I. hospitalis, which might be responsible for membrane dynamics. Overall, this unusual cellular compartmentalization, ultrastructure and dynamics in an archaeon that belongs to the recently proposed TACK superphylum prompts speculation that the eukaryotic endomembrane system might originate from Archaea.

Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm

Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning) and scanning electron microscopy (SEM) in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 μm diameter), arranged in a regular pattern (1.0-2.0 μm distance from cell to cell), whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS) were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005) protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.

Atopic dermatitis, STAT3- and DOCK8-hyper-IgE syndromes differ in IgE-based sensitization pattern

BACKGROUND

Increased serum IgE levels are characteristic but not specific for allergic diseases. Particularly, severe atopic dermatitis (AD) overlaps with hyper-IgE syndromes (HIES) regarding eczema, eosinophilia, and increased serum IgE levels. HIES are primary immunodeficiencies due to monogenetic defects such as in the genes DOCK8 and STAT3. As it is not known to date why allergic manifestations are not present in all HIES entities, we assessed the specificity of serum IgE of AD and HIES patients in the context of clinical and immunological findings.

METHODS

Clinical data, skin prick tests, specific IgE to aero- and food allergens, and T helper (Th) subpopulations were compared in AD and molecularly defined HIES patients.

RESULTS

Total serum IgE levels were similarly increased in STAT3-HIES, DOCK8-HIES, and AD patients. The ratio of aeroallergen-specific IgE to total IgE was highest in AD, whereas DOCK8-HIES patients showed the highest specific serum IgE against food allergens. Overall, clinical allergy and skin prick test results complied with the specific IgE results. Th2-cell numbers were significantly increased in DOCK8-HIES and AD patients compared to STAT3-HIES patients and controls. AD patients showed significantly higher nTreg-cell counts compared to STAT3-HIES and control individuals. High Th17-cell counts were associated with asthma. Specific IgE values, skin prick test, and T-cell subsets of STAT3-HIES patients were comparable with those of healthy individuals except decreased Th17-cell counts.

CONCLUSION

Hyper-IgE syndromes and atopic dermatitis patients showed different sensitization pattern of serum IgE corresponding to the allergic disease manifestations and Th-cell subset data, suggesting a key role of DOCK8 in the development of food allergy.

Cellular injuries upon exposure of Escherichia coli and Lactobacillus rhamnosus to high-intensity ultrasound

AIMS

To examine cellular injuries occurring in cells of Escherichia coli (Gram-negative bacteria) and Lactobacillus rhamnosus (Gram-positive bacteria) in response to a high-intensity ultrasound treatment using classical plate count technique and flow cytometry.

METHOD AND RESULTS

According to plate count results, E. coli (D-value 8.3 min) was far more sensitive than L. rhamnosus (D-value 18.1 min) in their response to the ultrasound intensity applied (20 kHz, 17.6 W). The dye precursor carboxyfluorescein diacetate (cFDA) could freely diffuse across the cytoplasmic membrane of intact cells of Gram-positive bacteria L. rhamnosus, resulting in its intracellular enzymatic conversion and emission of green fluorescence. In contrast, the presence of an outer membrane on E. coli, which represents the class of Gram-negative bacteria, apparently disabled the penetration of viability marker cFDA. Ultrasound application on E. coli yielded in an increasing population with disintegrated outer membrane, which allowed penetration of cFDA and its intracellular enzymatic conversion as well as accumulation. In both organisms evaluated only a small population was labelled by propidium iodide upon exposure to ultrasound for up to 20 min. Within the experimental conditions investigated ultrasound did not considerably affect the cytoplasmic membrane, although according to plate count results viability loss occurred.

CONCLUSIONS

The results compiled suggest, that ultrasound induced cell death, which may not be related to membrane damage.

SIGNIFICANCE AND IMPACT OF THE STUDY

Limitation on the use of bacteriocins, which are aimed on destabilization of cytoplasmic membrane but inhibited by the outer membrane, could be overcome by ultrasound-assisted physical disruption of the outer membrane.

Metastable States of Water and Ice during Pressure-Supported Freezing of Potato Tissue

Different ice modifications were obtained during freezing processes at several pressure levels from atmospheric pressure up to 300 MPa. In the pressure range between 210 and 240 MPa, a metastable ice I modification area was observed, as the nucleation of ice I crystals in the thermodynamically stable region of ice III was reached. A significant degree of supercooling was obtained before freezing the tissue water to ice III, which has to be considered when designing pressure-supported freezing processes. The effect of supercooling phenomenon on the phase transition time is discussed using a mathematical model based on the solution of the heat transfer governing differential equations. Phase transition and freezing times for the different freezing paths experimented are compared for the processes: freezing at atmospheric pressure, pressure-assisted freezing, and pressure-shift freezing. Different metastable states of liquid water are defined according to their process-dependent stability.

Sludge pre-treatment with pulsed electric fields

The anaerobic stabilization process depends - among other things - on the bio-availability of organic carbon. Through pre-treatment of the sludge which leads to the destruction of micro-organisms and to the setting-free of cell content substances (disintegration), the carbon can be microbially converted better and faster. Moreover, effects on the digestion are likely. However, only little experience is available in sludge treatment with pulsed electric fields. Laboratory-scale digestion tests have been run to analyse the influence of pulsed electric fields on the properties of sludge, anaerobic degradation, sludge water reload and foaming of digesters. The results will be compared with those of other disintegration methods (high pressure homogeniser, thermal treatment). The effect of pre-treatment on the sludge is shown by the COD release. Degrees of disintegration have been achieved up to 20%. The specific energy input was high. The energy consumption has been decreased by initial improvements (pre-heating to 55 degrees C). The filament bacteria were partially destroyed. The foam reduction in the digesters was marginal. The anaerobic degradation performance has been improved in every case. The degradation rate of organic matter increased about 9%. Due to the increase of degradation, there is a higher reload of the sludge-water with COD and nitrogen compounds.

Measurement of glutathione in activated sludges

Thermal, electric, mechanical or oxidative stress seem a promising way to reduce the production of excess activated sludge during biological wastewater treatment. However, the adaptation and the resistance of the sludge microbial ecosystem to stress conditions is a major question as it may definitively limit the effect of some treatments. Defence mechanisms developed by aerobic organisms, in particular, in response to oxidative stress involve various antioxidant activities and compounds such as glutathione. An HPLC method was developed for measuring reduced and total glutathione (GSH and GSHt) in perchloric acid sludge extracts. The method was sensitive, highly specific and validated for linearity, precision and recovery. Considering the extraction yield and the oxidation of GSH during extract storage, the measured GSH concentration was estimated to represent 60% of the GSH content from activated sludges. GSHt ranged from 0.32 to 3.34micromolg(-1) volatile solids and the GSH/GSHt ratio ranged from 32% to 91%. Measurements performed on sludges stressed in precise conditions selected to reach a reduction of sludge production showed a decrease of GSH and GSHt concentrations with thermal, mechanical, electric and ozone stress.

Application of ultrasound-assisted thermal processing for preservation and quality retention of liquid foods

A continuously working pilot plant-scale prototype was used to evaluate the effects of continuous-flow ultrasound-temperature treatment for bacterial decontamination of model suspensions and various liquid food systems such as milk, fruit, and vegetable juices. Escherichia coli K12 DH 5 alpha and Lactobacillus acidophilus were used as test microorganisms. In addition, treated juices were investigated for damage caused by heat or ultrasound-induced degradation of sensory and nutritional properties after treatment and storage. Changes in color and destruction of heat-labile and slightly oxidizable L-ascorbic acid content were monitored as an index to measure processing effects. Results were assessed with respect to the total energy requirement and compared with those using a conventional, indirect heating method having similar processing conditions. For the bacteriological process evaluation, the temperature- and time-dependent process lethality was used as the basis; for the quality- and energy-related investigations, the degree of bacterial inactivation was used. At identical degrees of bacterial inactivation, the ultrasound-assisted thermal treatments required a lower processing temperature than treatment with conventional thermal processing. However, according to energy balances, the total energy consumption was not reduced compared to conventional heating. Indications for a positive influence on shelf life, with improvements in surface color stability (lightness) and L-ascorbic acid retention, were found among quality parameters of treated orange juice.

Effects of pulsed electric fields on inactivation and metabolic activity of Lactobacillus plantarum in model beer

AIMS

Inactivation and sublethal injury of Lactobacillus plantarum at different pulsed electric field (PEF) strengths and total energy inputs were investigated to differentiate reversible and irreversible impacts on cell functionality.

METHODS AND RESULTS

Lactobacillus plantarum was treated with PEF in model beer (MB) to determine critical values of field strength and energy input for cell inactivation. Below critical values, metabolic activity and membrane integrity were initially reduced without loss of viability. Above critical values, however, irreversible cell damage occurred. Presence of nisin or hop extract, during PEF treatment, resulted in an additional reduction of cell viability by 1;5 log cycles. Also, addition of the hop extract resulted in an additional two log cycles of sublethal injury. Partial reversibility of membrane damage was observed using propidium iodide (PI) uptake and staining. Inoculated MB containing hops was stored after PEF to evaluate the efficacy of such treatment for beer preservation.

CONCLUSION

Cells were inactivated only above critical values of 13 kV x cm(-1) and 64 kJ x kg(-1); below these values cell damage was reversible. Storage experiments revealed that surviving cells were killed after 15 h storage in MB containing hops.

SIGNIFICANCE AND IMPACT OF THE STUDY

Both reversible and irreversible cell damage due to PEF treatment was detected, depending on specific treatment conditions. The combination of PEF and hop addition is a promising nonthermal method of preservation for beer.

Nutritional improvement of plant foods by non-thermal processing

As a result of the increasing consumer demand for minimally-processed fresh-like food products with high sensory and nutritional qualities, there is a growing interest in non-thermal processes for food processing and preservation. Key advanced technologies such as high-pressure processing, pulsed electric fields, dense gases and ultrasound are being applied to develop gentle but targeted processes to further improve the quality and safety of processed foods. These technologies also offer the potential for improving existing processes as well as for developing new process options. Furthermore, by adding new process dimensions (such as hydrostatic pressure, electric fields, ultrasonics, supercritical CO2) to the conventional process variables of temperature and time, they facilitate enlargement of the availability of unit operations. These operations might be applied effectively in unique combination processes, or as subsequent processing tools in more-targeted and subsequently less-intensive processes for food preservation and modification than the currently-applied processes.

Biphasic inactivation kinetics of Escherichia coli in liquid whole egg by high hydrostatic pressure treatments

Kinetic studies on the isothermal high hydrostatic pressure (HHP) inactivation of Escherichia coli in liquid whole egg (LWE) were performed at 5 and 25 degrees C in the pressure range of 250-400 MPa. The characteristic tailing inactivation curves were described by a first-order biphasic model. As compared to a previous rheological study, it is suggested that the phase change of LWE during pressure treatment affects the inactivation rate of E. coli. Within the processing criteria where the rheological properties of LWE were still comparable to those of fresh LWE, HHP treatments at 5 degrees C induced more E. coli inactivations than those at 25 degrees C. From the results of approximately 3 log reductions of E. coli and over 5 log reductions of Pseudomonas and Paenibacillus, HHP treatment of LWE at 5 degrees C is regarded to be as effective as conventional thermal pasteurization. However, no post-process contamination and the consistency of temperature during preparation, HHP treatment, and storage provide clear processing advantages.