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A novel interdomain consortium composed of a methanogenic Archaeon and a sulfate-reducing bacterium was isolated from a microbial biofilm in an oil well in Cahuita National Park, Costa Rica. Both organisms can be grown in pure culture or as stable co-culture. The methanogenic cells were non-motile rods producing CH4 exclusively from H2/CO2. Cells of the sulfate-reducing partner were motile rods forming cell aggregates. They utilized hydrogen, lactate, formate, and pyruvate as electron donors. Electron acceptors were sulfate, thiosulfate, and sulfite. 16S rRNA sequencing revealed 99% gene sequence similarity of strain CaP3V-M-L2AT to Methanobacterium subterraneum and 98.5% of strain CaP3V-S-L1AT to Desulfomicrobium baculatum. Both strains grew from 20 to 42 °C, pH 5.0–7.5, and 0–4% NaCl. Based on our data, type strains CaP3V-M-L2AT (= DSM 113354 T = JCM 39174 T) and CaP3V-S-L1AT (= DSM 113299 T = JCM 39179 T) represent novel species which we name Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov.

A major aim in structural cell biology is to analyze intact cells in three dimensions, visualize subcellular structures, and even localize proteins at the best possible resolution in three dimensions. Though recently developed electron microscopy tools such as electron tomography, or three-dimensional (3D) scanning electron microscopy, offer great resolution in three dimensions, the challenge is that, the better the resolution, usually the smaller the volume under investigation. Several different approaches to overcome this challenge were presented at the Microscopy Conference in Vienna in 2021. These tools include array tomography, batch tomography, or scanning transmission electron tomography, all of which can nowadays be extended toward correlative light and electron tomography, with greatly increased 3D information. Here, we review these tools, describe the underlying procedures, and discuss their advantages and limits.

Radiation of ionizing or non-ionizing nature has harmful effects on cellular components like DNA as radiation can compromise its proper integrity. To cope with damages caused by external stimuli including radiation, within living cells, several fast and efficient repair mechanisms have evolved. Previous studies addressing organismic radiation tolerance have shown that radiotolerance is a predominant property among extremophilic microorganisms including (hyper-) thermophilic archaea. The analysis of the ionizing radiation tolerance of the chemolithoautotrophic, obligate anaerobic, hyperthermophilic Crenarchaeon Ignicoccus hospitalis showed a D10-value of 4.7 kGy, fourfold exceeding the doses previously determined for other extremophilic archaea. The genome integrity of I. hospitalis after γ-ray exposure in relation to its survival was visualized by RAPD and qPCR. Furthermore, the discrimination between reproduction, and ongoing metabolic activity was possible for the first time indicating that a potential viable but non-culturable (VBNC) state may also account for I. hospitalis.

In previous publications, it was hypothesized that Micrarchaeota cells are covered by two individual membrane systems. This study proves that at least the recently cultivated “Candidatus Micrarchaeum harzensis A_DKE” possesses an S-layer covering its cytoplasmic membrane. The potential S-layer protein was found to be among the proteins with the highest abundance in “Ca. Micrarchaeum harzensis A_DKE,” and in silico characterization of its primary structure indicated homologies to other known S-layer proteins. Homologues of this protein were found in other Micrarchaeota genomes, which raises the question of whether the ability to form an S-layer is a common trait within this phylum. The S-layer protein seems to be glycosylated, and the micrarchaeon expresses genes for N-glycosylation under cultivation conditions, despite not being able to synthesize carbohydrates. Electron micrographs of freeze-etched samples of a previously described coculture, containing “Ca. Micrarchaeum harzensis A_DKE” and a Thermoplasmatales member as its host organism, verified the hypothesis of an S-layer on the surface of “Ca. Micrarchaeum harzensis A_DKE.” Both organisms are clearly distinguishable by cell size, shape, and surface structure. IMPORTANCE Our knowledge about the DPANN superphylum, which comprises several archaeal phyla with limited metabolic capacities, is mostly based on genomic data derived from cultivation-independent approaches. This study examined the surface structure of a recently cultivated member “Candidatus Micrarchaeum harzensis A_DKE,” an archaeal symbiont dependent on an interaction with a host organism for growth. The interaction requires direct cell contact between interaction partners, a mechanism which is also described for other DPANN archaea. Investigating the surface structure of “Ca. Micrarchaeum harzensis A_DKE” is an important step toward understanding the interaction between Micrarchaeota and their host organisms and living with limited metabolic capabilities, a trait shared by several DPANN archaea.

Archaea swim by means of a unique molecular machine called the archaellum. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament, allowing the cell to rapidly propel itself through liquid media.The archaellum filament comprises multiple copies of helically organised subunits named archaellins. While in many species several archaellin homologs are encoded in the same operon, structural studies conducted to date have suggested that archaella consist of only one protein species. Thus, the role of the remaining archaellin genes remains elusive.Here we present the structure of the Methanocaldococcus villosus archaellum filament at 3.08 Å resolution. We find that the filament is composed of two alternating archaellins - ArlB1 and ArlB2, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify two major structural elements that enable the archaellum filament to move.Our findings provide new insights into archaeal motility and challenge the current view on the archaellum architecture and assembly.

Background Doxorubicin is a cytostatic drug from the group of anthracycline antibiotics that is widely used as a chemotherapeutic agent. Side effects of the active substance include cardiotoxicity and nephrotoxicity. Doxorubicin-treated renal epithelial cells and (sarcoma) tumors are examined by correlative light and electron microscopy (CLEM) to investigate the subcellular localization of doxorubicin. Methods The kidney epithelial cell line MDCK II (Madin-Darby Canine Kidney) grown on culture dishes were treated with doxorubicin. Subsequently, the cells are analyzed by means of fluorescence and transmission electron microscopy (TEM). In vivo, alveolar rhabdomyosarcoma (RH 30) tumor cells are transferred to the chorioallantoic membrane (CAM) of the chicken embryo. Doxorubicin is injected into a vein of the chicken embryo. After 24 hours, the tumor is removed and examined using CLEM. Results The kidney epithelial cells and the doxorubicin-injected tumors show a clear staining of the cell nucleus, which correlates with electron-dense regions (heterochromatin). High-resolution TEM shows that doxorubicin treatment leads to an enormous stress situation with an increased formation of membrane blebbings. Conclusions CLEM is a promising new method to visualize the pattern of fluorescing drugs (e.g. doxorubicin) in renal epithelial cells and tumors, and to localize the drug in its subcellular context combined with high resolution.

The prokaryotic cell is traditionally seen as a ���bag of enzymes,��� yet its organization is much more complex than in this simplified view. By now, various microcompartments encapsulating metabolic enzymes or pathways are known for Bacteria. These microcompartments are usually small, encapsulating and concentrating only a few enzymes, thus protecting the cell from toxic intermediates or preventing unwanted side reactions. The hyperthermophilic, strictly anaerobic Crenarchaeon Ignicoccus hospitalis is an extraordinary organism possessing two membranes, an inner and an energized outer membrane. The outer membrane (termed here outer cytoplasmic membrane) harbors enzymes involved in proton gradient generation and ATP synthesis. These two membranes are separated by an intermembrane compartment, whose function is unknown. Major information processes like DNA replication, RNA synthesis, and protein biosynthesis are located inside the ���cytoplasm��� or central cytoplasmic compartment. Here, we show by immunogold labeling of ultrathin sections that enzymes involved in autotrophic CO2 assimilation are located in the intermembrane compartment that we name (now) a peripheric cytoplasmic compartment. This separation may protect DNA and RNA from reactive aldehydes arising in the I. hospitalis carbon metabolism. This compartmentalization of metabolic pathways and information processes is unprecedented in the prokaryotic world, representing a unique example of spatiofunctional compartmentalization in the second domain of life.

Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses.

Micrarchaeota are members of the archaeal DPANN superphylum. These so far poorly characterized archaea have been found to have reduced genomes and likely depend on interactions with host organisms for growth and survival. Here we report on the enrichment of the first stable co-culture of a member of the Micrarchaeota together with its host, as well as the isolation of the latter. Electron microscopic analysis suggest that growth is dependent on the physical interaction of the two organisms within a biofilm. The interaction seems to be ensured by the necessity to grow in form of a biofilm. Furthermore, transcriptomic analyses indicate a shift towards biofilm formation of the host as a result of co-cultivation. Finally, genomic, metabolomic, extracellular polymeric substance (EPSs) and lipid content analyses reveal that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host and thereby provide first insights into the basis of symbiont-host interactions.

Abstract Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. # Description of contents of this directory ## 1_Genomes.tar.gz Contains the protein files used for the annotations and to extract certain proteins for phylogenetic analyses. ## 2_Annotations.tar.gz This folder contains the full workflow to annotate the genomes of interest and a jupyter lab book (python3) used for parsing the data. Additionally, this folder contains: 0_Dependencies: Any custom scripts used as well as databases and mapping files (only provided if databases were modified) 1_Input: Output of the annotation workflow as well as any mapping file required by the python3 script to further parse the data 2_Output: Parsed annotation table ## 3_Phylogenies.tar.gz Contains all files generated for the phylogenies of certain lipid genes. These files are provided for the archaea only and the universal analysis (see Methods of the main paper for details). Each foldercontains: required scripts and mapping files raw sequences (protein, faa), separate for each lipid gene of interest. These come in individual versions: indiv: sequences for all arcogs final: sequences for arcogs and if several arcogs were assigned to the same COG, these arCOGs were combined into one file. If arCOGs were combined, this is listed in the provided overview table in the main directory. aligned sequences aligned and trimmed sequences output from IQ-TREE PDFs for each individual tree ## 4_raw data_ARMAN lipids Lipid extracts were analyzed by UHPLC–atmospheric pressure chemical ionization (APCI) MS for archaeal core lipids, including archaeol (diether, C20 isoprenoid chains) and glycerol dialkyl glycerol tetraether (GDGTs, tetraether, C40 side chain), according to Hopmans et al., 2016 (Organic geochemistry 93:1-6), with some modifications. Briefly, the analysis was performed on an Agilent 1260 UHPLC coupled to a 6130 quadrupole MSD in selected ion monitoring (SIM) mode. Files provided here are raw data files out of these analyses: Ca. Scheffleriplasma hospitalis Bligh&Dyer total lipid extract (U1808198) analysis includes the core lipid analysis of those present in the culture; Ca. Scheffleriplasma hospitalis Bligh&Dyer total lipid extract after acid hydrolysis (U1809068) includes the intact polar-lipid-derived core lipids plus the core lipids of the previous analysis run. Run U1809060 corresponds to the run of the Bligh&Dyer total lipid extract of the co-culture of Ca. Micrarchaeum harzensis and Ca. Scheffleriplasma hospitalis, including the present core lipids. Run U1809066, corresponds to the run of the Bligh&Dyer total lipid extract after acid hydrolysis of the co-culture of Ca. Micrarchaeum harzensis and Ca. Scheffleriplasma hospitalis, including the the intact polar-lipid-derived core lipids plus the core lipids of the previous analysis run. - Comment for Version 2: We forgot to upload files in a subfolder in 3_Phylogenies and provide them now in this updated version. - Comment for Version 3: Added some new data (4_raw data_ARMAN lipids)

In previous publications, it was hypothesized that Micrarchaeota cells are covered by two individual membrane systems. This study proofs that at least the recently cultivated “Candidatus Micrarchaeum harzensis A_DKE” possesses an S-layer covering its cytoplasmic membrane. The potential S-layer protein was found to be among the proteins with the highest abundance in A_DKE and in silico characterization of its primary structure indicated homologies to other known S-layer proteins. Homologs of this protein were found in other Micrarchaeota genomes, which raises the question, whether the ability to form an S-layer is a common trait within this phylum. The S-layer protein seems to be glycosylated and the Micrarchaeum expresses genes for N-glycosylation under cultivation conditions, despite not being able to synthesize carbohydrates. Electron micrographs of freeze-etched samples of a previously described co-culture, containing Micrarchaeum A_DKE and a Thermoplasmatales member as its host organism, verified the hypothesis of an S-layer on the surface of A_DKE. Both organisms are clearly distinguishable by cell size, shape and surface structure.

The application of both fluorescence and electron microscopy results in a powerful combination of imaging modalities called "correlative light and electron microscopy" (CLEM). Whereas conventional transmission electron microscopy (TEM) tomography is only able to image sections up to a thickness of ~300nm, scanning transmission electron microscopy (STEM) tomography at 200kV allows the analysis of sections up to a thickness of 900nm in three dimensions. In the current study we have successfully integrated STEM tomography into CLEM as demonstrated for human retinal pigment epithelial 1 (RPE1) cells expressing various fluorescent fusion proteins which were high-pressure frozen and then embedded in Lowicryl HM20. Fluorescently labeled gold nanoparticles were applied onto resin sections and imaged by fluorescence and electron microscopy. STEM tomograms were recorded at regions of interest, and overlays were generated using the eC-CLEM software package. Through the nuclear staining of living cells, the use of fluorescently labeled gold fiducials for the generation of overlays, and the integration of STEM tomography we have markedly extended the application of the Kukulski protocol (Kukulski et al., 2011, 2012). Various fluorescently tagged proteins localizing to different cellular organelles could be assigned to their ultrastructural compartments. By combining STEM tomography with on-section CLEM, fluorescently tagged proteins can be localized in three-dimensional ultrastructural environments with a volume of at least 2.7×2.7×0.5μm.

The application of both fluorescence and electron microscopy results in a powerful combination of imaging modalities called "correlative light and electron microscopy" (CLEM). Whereas conventional transmission electron microscopy (TEM) tomography is only able to image sections up to a thickness of ~300nm, scanning transmission electron microscopy (STEM) tomography at 200kV allows the analysis of sections up to a thickness of 900nm in three dimensions. In the current study we have successfully integrated STEM tomography into CLEM as demonstrated for human retinal pigment epithelial 1 (RPE1) cells expressing various fluorescent fusion proteins which were high-pressure frozen and then embedded in Lowicryl HM20. Fluorescently labeled gold nanoparticles were applied onto resin sections and imaged by fluorescence and electron microscopy. STEM tomograms were recorded at regions of interest, and overlays were generated using the eC-CLEM software package. Through the nuclear staining of living cells, the use of fluorescently labeled gold fiducials for the generation of overlays, and the integration of STEM tomography we have markedly extended the application of the Kukulski protocol (Kukulski et al., 2011, 2012). Various fluorescently tagged proteins localizing to different cellular organelles could be assigned to their ultrastructural compartments. By combining STEM tomography with on-section CLEM, fluorescently tagged proteins can be localized in three-dimensional ultrastructural environments with a volume of at least 2.7×2.7×0.5μm.

Vitamin C is an essential nutrient for humans and is involved in a plethora of health-related functions. Several studies have shown a connection between vitamin C intake and an improved resistance to infections that involves the immune system. However, the body cannot store vitamin C and both the elevated oral intake, and the intravenous application have certain disadvantages. In this study, we wanted to show a new formulation for the liposomal packaging of vitamin C. Using freeze etching electron microscopy, we show the formed liposomes. With a novel approach of post-processing procedures of real-time sonography that combines enhancement effects by contrast-like ultrasound with a transducer, we wanted to demonstrate the elevated intestinal vitamin C resorption on four participants. With the method presented in this study, it is possible to make use of the liposomal packaging of vitamin C with simple household materials and equipment for intake elevation. For the first time, we show the enhanced resorption of ingested liposomes using microbubble enhanced ultrasound imaging.

The interpretation of cell biological processes hinges on the elucidation of the underlying structures. Their three-dimensional analysis using electron tomography has extended our understanding of cellular organelles tremendously. The investigations depend on the availability of appropriate instruments for data recording. So far, such investigations have been done to a great extent on 300 keV transmission electron microscopes. Here we show the implementation of STEM tomography on a 200 kV FEG transmission electron microscope, including the tuning of the condenser for forming a beam with a small illumination aperture, dual-axis data recording, and evaluation of the maximum sample thickness and quality of the data. Our results show that the approach is accomplishable and promising, with high reliability, and reaching excellent data quality from plastic sections with a thickness of at least 900 nm.

Significance The passive translocation mechanism of arginine-rich cell-penetrating peptides has puzzled the scientific community for more than 20 y. In this study we propose a hitherto unrecognized mechanism of passive cell entry involving fusion of multilamellar structures generated by the cell-penetrating peptides. The geometry of entry for this mechanism is completely different from previously suggested direct translocation mechanisms, leading to another paradigm for designing molecular carriers for drug delivery to the cell., 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.

Mammalian podocytes, the key determinants of the kidney's filtration barrier, differentiate from columnar epithelial cells and several key determinants of apical-basal polarity in the conventional epithelia have been shown to regulate podocyte morphogenesis and function. However, little is known about the role of Crumbs, a conserved polarity regulator in many epithelia, for slit-diaphragm formation and podocyte function. In this study, we used Drosophila nephrocytes as model system for mammalian podocytes and identified a conserved function of Crumbs proteins for cellular morphogenesis, nephrocyte diaphragm assembly/maintenance, and endocytosis. Nephrocyte-specific knock-down of Crumbs results in disturbed nephrocyte diaphragm assembly/maintenance and decreased endocytosis, which can be rescued by Drosophila Crumbs as well as human Crumbs2 and Crumbs3, which were both expressed in human podocytes. In contrast to the extracellular domain, which facilitates nephrocyte diaphragm assembly/maintenance, the intracellular FERM-interaction motif of Crumbs is essential for regulating endocytosis. Moreover, Moesin, which binds to the FERM-binding domain of Crumbs, is essential for efficient endocytosis. Thus, we describe here a new mechanism of nephrocyte development and function, which is likely to be conserved in mammalian podocytes.

The anaerobic, non-motile strain HMT was isolated from the naphthalene-degrading, sulfate-reducing enrichment culture N47. For 20 years, strain HMT has been a stable member of culture N47 although it is neither able to degrade naphthalene nor able to reduce sulfate in pure culture. The highest similarity of the 16S rRNA gene sequence of strain HMT (89 %) is with a cultivated member of the family Spirochaetaceae , Treponema caldarium strain H1T (=DSM 7334T), an obligately anaerobic, thermophilic spirochaete isolated from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA. In contrast to this strain and the majority of spirochaete species described, strain HMT showed a rod-shaped morphology. Growth occurred at temperatures between 12 and 50 °C (optimum 37 °C) but the isolate was not able to grow at 60 °C. The strain fermented various sugars including d-glucose, d-fructose, lactose and sucrose. Addition of 0.1 % (w/v) yeast extract or 0.1 % (w/v) tryptone to the culture medium was essential for growth and could not be replaced by either the vitamin solutions tested or by 0.1 % (w/v) peptone or 0.1 % (w/v) casamino acids. The DNA G+C content of the isolate was 51.5 mol%. The major fatty acids were C14 : 0, C18 : 1ω13c, C16 : 1ω9t, C16 : 1ω11c and C16 : 1ω9c. Based on the unique morphology and the phylogenetic distance from the closest cultivated relative, a novel genus and species, Rectinema cohabitans gen. nov., sp. nov., is proposed. The type strain is strain HMT (=DSM 100378T=JCM 30982T).

For nearly 50 years immunogold labeling on ultrathin sections has been successfully used for protein localization in laboratories worldwide. In theory and in practice, this method has undergone continual improvement over time. In this study, we carefully analyzed circulating protocols for postembedding labeling to find out if they are still valid under modern laboratory conditions, and in addition, we tested unconventional protocols. For this, we investigated immunolabeling of Epon-embedded cells, immunolabeling of cells treated with osmium, and the binding behavior of differently sized gold particles. Here we show that (in contrast to widespread belief) immunolabeling of Epon-embedded cells and of cells treated with osmium tetroxide is actually working. Furthermore, we established a "speed protocol" for immunolabeling by reducing antibody incubation times. Finally, we present our results on three-dimensional immunogold labeling.

This study examined the influence of prior salt adaptation on the survival rate of (hyper)-thermophilic bacteria and archaea after desiccation and UV or ionizing irradiation treatment. Survival rates after desiccation of Hydrogenothermus marinus and Archaeoglobus fulgidus increased considerably when the cells were cultivated at higher salt concentrations before drying. By doubling the concentration of NaCl, a 30 times higher survival rate of H. marinus after desiccation was observed. Under salt stress, the compatible solute diglycerol phosphate in A. fulgidus and glucosylglycerate in H. marinus accumulated in the cytoplasm. Several different compatible solutes were added as protectants to A. fulgidus and H. marinus before desiccation treatment. Some of these had similar effects as intracellularly produced compatible solutes. The survival rates of H. marinus and A. fulgidus after exposure to UV-C (254 nm) or ionizing X-ray/gamma radiation were irrespective of the salt-induced synthesis or the addition of compatible solutes.

Due to its structural and molecular similarities to mammalian podocytes, the Drosophila nephrocyte emerged as a model system to study podocyte development and associated diseases. Similar to podocytes, nephrocytes establish a slit diaphragm between foot process-like structures in order to filter the hemolymph. One major obstacle in nephrocyte research is the distinct visualization of this subcellular structure to assess its integrity. Therefore, we developed a specialized dissection and fixation protocol, including high pressure freezing and freeze substitution techniques, to improve the preservation of the intricate ultrastructural details necessary for electron microscopic assessment. By means of scanning transmission electron microscopy (STEM) tomography, a three-dimensional dataset was generated to further understand the complex architecture of the nephrocyte channel system. Moreover, a staining protocol for immunolabeling of ultrathin sections of Epon-embedded nephrocytes is discussed, which allows the reliable detection of GFP-tagged fusion proteins combined with superior sample preservation. Due to the growing number of available GFP-trap fly lines, this approach is widely applicable for high resolution localization studies in wild type and mutant nephrocytes.

Three different multihaem cytochromes c were purified from cell extracts of the hyperthermophilic archaeon Ignicoccus hospitalis. One tetrahaem cytochrome, locus tag designation Igni_0530, was purified from membrane fractions together with the iron–sulfur protein Igni_0529. Two octahaem cytochromes, Igni_0955 and Igni_1359, were purified from soluble fractions but were also present in the membrane fraction. N-terminal sequencing showed that three of the four proteins had their signal peptides cleaved off, while results were ambiguous for Igni_0955. In contrast, mass spectrometry of Igni_0955 and Igni_1359 resulted in single mass peaks including the signal sequences and eight haems per subunit and so both forms might be present in the cell. Igni_0955 and Igni_1359 belong to the hydroxylamine dehydrogenase (HAO) family (29 % mutual identity). HAO or reductase activities with inorganic sulfur compounds were not detected. Igni_0955 was reduced by enriched I. hospitalis hydrogenase at a specific activity of 243 nmol min−1 (mg hydrogenase)−1 while activity was non-existent for Igni_0530 and low for Igni_1359. Immuno-electron microscopy of ultra-thin sections showed that Igni_0955 and Igni_1359 are located in both I. hospitalis membranes and also in the intermembrane compartment. We concluded that these cytochromes might function as electron shuttles between the hydrogenase in the outer cellular membrane and cellular reductases, whereas Igni_0530 might be part of the sulfur-reducing mechanism.

The mode of renin release from renal juxtaglomerular cells into circulation is still unsolved in several aspects. Here we studied the intracellular organization of renin-storage vesicles and their changes during controlled stimulation of renin release. This was accomplished using isolated perfused mouse kidneys with 3-dimensional electron microscopic analyses of renin-producing cells. Renin was found to be stored in a network of single granules and cavern-like structures, and dependent on the synthesis of glycosylated prorenin. Acute stimulation of renin release led to increased exocytosis in combination with intracellular fusion of vesicles to larger caverns and their subsequent emptying. Renin release from the kidneys of SCID-beige mice, which contain few but gigantic renin-storage vesicles, was no different from that of kidneys from wild-type mice. Thus, our findings suggest that renin is released by mechanisms similar to compound exocytosis.

The bacterial flagellar apparatus, which involves ∼40 different proteins, has been a model system for understanding motility and chemotaxis. The bacterial flagellar filament, largely composed of a single protein, flagellin, has been a model for understanding protein assembly. This system has no homology to the eukaryotic flagellum, in which the filament alone, composed of a microtubule-based axoneme, contains more than 400 different proteins. The archaeal flagellar system is simpler still, in some cases having ∼13 different proteins with a single flagellar filament protein. The archaeal flagellar system has no homology to the bacterial one and must have arisen by convergent evolution. However, it has been understood that the N-terminal domain of the archaeal flagellin is a homolog of the N-terminal domain of bacterial type IV pilin, showing once again how proteins can be repurposed in evolution for different functions. Using cryo-EM, we have been able to generate a nearly complete atomic model for a flagellar-like filament of the archaeon Ignicoccus hospitalis from a reconstruction at ∼4-A resolution. We can now show that the archaeal flagellar filament contains a β-sandwich, previously seen in the FlaF protein that forms the anchor for the archaeal flagellar filament. In contrast to the bacterial flagellar filament, where the outer globular domains make no contact with each other and are not necessary for either assembly or motility, the archaeal flagellin outer domains make extensive contacts with each other that largely determine the interesting mechanical properties of these filaments, allowing these filaments to flex.

The Crenarchaeon Ignicoccus hospitalis lives in symbiosis with Nanoarchaeum equitans providing essential cell components and nutrients to its symbiont. Ignicoccus hospitalis shows an intriguing morphology that points toward an evolutionary role in driving compartmentalization. Therefore, the bioenergetics of this archaeal host-symbiont system remains a pressing question. To date, the only electron acceptor described for I. hospitalis is elemental sulfur, but the organism comprises genes that encode for enzymes involved in nitrogen metabolism, e.g., one nitrate reductase and two octaheme cytochrome c, Igni_0955 (IhOCC) and Igni_1359. Herein, we detail functional and structural studies of the highly abundant IhOCC, including an X-ray crystal structure at 1.7 Å resolution, the first three-dimensional structure of an archaeal OCC. The trimeric IhOCC is membrane associated and exhibits significant structural and functional differences to previously characterized homologs within the hydroxylamine oxidoreductases (HAOs) and octaheme cytochrome c nitrite reductases (ONRs). The positions and spatial arrangement of the eight hemes are highly conserved, but the axial ligands of the individual hemes 3, 6 and 7 and the protein environment of the active site show significant differences. Most notably, the active site heme 4 lacks porphyrin-tyrosine cross-links present in the HAO family. We show that IhOCC efficiently reduces nitrite and hydroxylamine, with possible relevance to detoxification or energy conservation.Structural data are available in the Protein Data Bank under the accession number 4QO5.

Candida albicans cells lacking the Pil1 and Lsp1 proteins needed to form eisosome microdomains in the plasma membrane develop deep cell wall invaginations. Overproduction of the Sur7 membrane protein rescues the defects of pil1Δ lsp1Δ cells, demonstrating that a key role for eisosomes is to promote Sur7 regulation of plasma membrane function., The plasma membrane of the fungal pathogen Candida albicans forms a protective barrier that also mediates many processes needed for virulence, including cell wall synthesis, invasive hyphal morphogenesis, and nutrient uptake. Because compartmentalization of the plasma membrane is believed to coordinate these diverse activities, we examined plasma membrane microdomains termed eisosomes or membrane compartment of Can1 (MCC), which correspond to ∼200-nm-long furrows in the plasma membrane. A pil1∆ lsp1∆ mutant failed to form eisosomes and displayed strong defects in plasma membrane organization and morphogenesis, including extensive cell wall invaginations. Mutation of eisosome proteins Slm2, Pkh2, and Pkh3 did not cause similar cell wall defects, although pkh2∆ cells formed chains of furrows and pkh3∆ cells formed wider furrows, identifying novel roles for the Pkh protein kinases in regulating furrows. In contrast, the sur7∆ mutant formed cell wall invaginations similar to those for the pil1∆ lsp1∆ mutant even though it could form eisosomes and furrows. A PH-domain probe revealed that the regulatory lipid phosphatidylinositol 4,5-bisphosphate was enriched at sites of cell wall invaginations in both the sur7∆ and pil1∆ lsp1∆ cells, indicating that this contributes to the defects. The sur7∆ and pil1∆ lsp1∆ mutants displayed differential susceptibility to various types of stress, indicating that they affect overlapping but distinct functions. In support of this, many mutant phenotypes of the pil1∆ lsp1∆ cells were rescued by overexpressing SUR7. These results demonstrate that C. albicans eisosomes promote the ability of Sur7 to regulate plasma membrane organization.

Because nanoparticles are finding uses in myriad biomedical applications, including the delivery of nucleic acids, a detailed knowledge of their interaction with the biological system is of utmost importance. Here the size-dependent uptake of gold nanoparticles (AuNPs) (20, 30, 50 and 80 nm), coated with a layer-by-layer approach with nucleic acid and poly(ethylene imine) (PEI), into a variety of mammalian cell lines is studied. In contrast to other studies, the optimal particle diameter for cellular uptake is determined but also the number of therapeutic cargo molecules per cell. It is found that 20 nm AuNPs, with diameters of about 32 nm after the coating process and about 88 nm including the protein corona after incubation in cell culture medium, yield the highest number of nanoparticles and therapeutic DNA molecules per cell. Interestingly, PEI, which is known for its toxicity, can be applied at significantly higher concentrations than its IC(50) value, most likely because it is tightly bound to the AuNP surface and/or covered by a protein corona. These results are important for the future design of nanomaterials for the delivery of nucleic acids in two ways. They demonstrate that changes in the nanoparticle size can lead to significant differences in the number of therapeutic molecules delivered per cell, and they reveal that the toxicity of polyelectrolytes can be modulated by an appropriate binding to the nanoparticle surface.

Ignicoccus hospitalis , a hyperthermophilic, chemolithoautotrophic crenarchaeon was found to possess a new CO 2 fixation pathway, the dicarboxylate/4-hydroxybutyrate cycle. The primary acceptor molecule for this pathway is acetyl coenzyme A (acetyl-CoA), which is regenerated in the cycle via the characteristic intermediate 4-hydroxybutyrate. In the presence of acetate, acetyl-CoA can alternatively be formed in a one-step mechanism via an AMP-forming acetyl-CoA synthetase (ACS). This enzyme was identified after membrane preparation by two-dimensional native PAGE/SDS-PAGE, followed by matrix-assisted laser desorption ionization–time of flight tandem mass spectrometry and N-terminal sequencing. The ACS of I. hospitalis exhibits a molecular mass of ∼690 kDa with a monomeric molecular mass of 77 kDa. Activity tests on isolated membranes and bioinformatic analyses indicated that the ACS is a constitutive membrane-associated (but not an integral) protein complex. Unexpectedly, immunolabeling on cells of I. hospitalis and other described Ignicoccus species revealed that the ACS is localized at the outermost membrane. This perfectly coincides with recent results that the ATP synthase and the H 2 :sulfur oxidoreductase complexes are also located in the outermost membrane of I. hospitalis . These results imply that the intermembrane compartment of I. hospitalis is not only the site of ATP synthesis but may also be involved in the primary steps of CO 2 fixation.

Upon slow crystallization from silica-containing solutions or gels at elevated pH, alkaline-earth carbonates spontaneously self-assemble into remarkable nanocrystalline ultrastructures. These so-called silica biomorphs exhibit curved morphologies beyond crystallographic symmetry and ordered textures reminiscent of the hierarchical design found in many biominerals. The formation of these fascinating materials is thought to be driven by a dynamic coupling of the components' speciations in solution, which causes concerted autocatalytic mineralization of silica-stabilized nanocrystals over hours. In the present work, we have studied the precipitation kinetics of this unique system by determining growth rates of individual aggregates using video microscopy, and correlated the results with time-dependent data on the concentration of metal ions and pH acquired online during crystallization. In this manner, insight to the evolution of chemical conditions during growth was gained. It is shown that crystallization proceeds linearly with time and is essentially reaction controlled, which fits well in the proposed morphogenetic scenario, and thus, indirectly supports it. Measurements of the silica concentration in solution, combined with analyses of crystal aggregates isolated at distinct stages of morphogenesis, further demonstrate that the fraction of silica coprecipitated with carbonate during active growth is rather small. We discuss our findings with respect to the role of silica in the formation of biomorphs, and moreover, prove that the external silica skins that occasionally sheath the aggregates--previously supposed to be involved in the growth mechanism--originate from secondary precipitation after growth is already terminated.

Nanoarchaeum equitans und Ignicoccus hospitalis sind anaerobe hyperthermophile Mikroorganismen. Sie reprasentieren eine einzigartige, rein archaeelle Lebensgemeinschaft, in der N. equitans zwingend auf seinen Wirt I. hospitalis angewiesen ist, da es alle seine Lipide und Aminosauren von ihm bezieht. I. hospitalis lebt von der Reduktion elementaren Schwefels mit Wasserstoff. Er besitzt einen neuen CO2-Fixierungsweg und eine fur Archaeen einmalige Zellstruktur aus innerer und auserer Membran, die zwei Zellkompartimente bilden, das Cytoplasma und einen grosen Intermembranraum. Durch immunologische Analysen zeigten wir, dass bei I. hospitalis die ATP-Synthase- und die H2:Schwefel-Oxidoreduktase-Komplexe in seiner auseren Membran lokalisiert sind. Damit ist er der erste Prokaryot mit einer energetisierten auseren Membran, ATP-Synthese auserhalb des Cytoplasmas und der raumlichen Trennung von Energiekonservierung und Informationsubertragung oder Proteinbiosynthese. Daraus ergeben sich zahlreiche Fragen zur Funktion und Charakterisierung der beiden Membranen und Zellkompartimente sowie einem moglichen Energietransfer zu N. equitans. An enigmatical association of two Archaea The obligate anaerobic hyperthermophilic Nanoarchaeum equitans and Ignicoccus hospitalis represent a unique, purely archaeal biocoenosis which is mandatory for N. equitans. Its strong dependence on I. hospitalis is affirmed by the fact that its lipids and amino acids are obtained exclusively from the host. The Crenarchaeon I. hospitalis is characterized by energy production via reduction of elemental sulfur with molecular hydrogen and a novel CO2-fixation pathway. It possesses a unique cell envelope for Archaea with an inner and an outer membrane, forming two cell compartments, the cytoplasm and a huge intermembrane compartment. By immuno-analyses we demonstrated that the ATP synthase and H2:sulfur oxidoreductase complexes of I. hospitalis are located in the outer membrane. Thus I. hospitalis is the first Prokaryote with an energized outer membrane, ATP synthesis outside the cytoplasm, and spatial separation of energy conservation from information processing and protein biosynthesis. This raises many questions on the function and characterization of the two membranes, the two cell compartments, and a possible ATP transfer to N. equitans.

We report on the effects of electrolytes spanning a range of anions (NaOc, NaSCN, NaNO(3), NaBr, NaCl, NaBu, NaOAc, Na(2)SO(4), Na(2)HPO(4), and Na(2)CO(3)) and cations (LiCl, NaCl, KCl, CsCl, and choline chloride) on the aqueous solubility of an extended surfactant. The surfactant is anionic with a long hydrophobic tail as well as a significant fraction of propylene oxide groups and ethylene oxide groups (C(12-14)-PO(16)-EO(2)-SO(4)Na, X-AES). In the absence of electrolytes, X-AES exhibits a cloud-point temperature that decreases with increasing surfactant concentration. After the addition of salts to the surfactant solutions, various shifts in the solubility curves are observed. These shifts follow precisely the same Hofmeister series that is found for salting-in and salting-out effects in protein solutions. In the presence of different concentrations of sodium xylene sulfonate (SXS), the solubility of the surfactant increases. In this context, SXS can be considered to be a salting-in salt. However, when the electrolytes are added to an aqueous solution of X-AES and SXS the Hofmeister series reverses for divalent anions such as Na(2)SO(4), Na(2)HPO(4), and Na(2)CO(3). Studies on the phase behavior and micelle structures using polarization microscopy, freeze-etch TEM, and NMR measurements indicate a dramatic change in the coexisting phases on the addition of SXS.

The plasma membrane of the yeast Saccharomyces cerevisiae contains stably distributed lateral domains of specific composition and structure, termed MCC ( m embrane c ompartment of arginine permease C an1). Accumulation of Can1 and other specific proton symporters within MCC is known to regulate the turnover of these transporters and is controlled by the presence of another MCC protein, Nce102. We show that in an NCE102 deletion strain the function of Nce102 in directing the specific permeases into MCC can be complemented by overexpression of the NCE102 close homolog FHN1 (the previously uncharacterized YGR131W ) as well as by distant Schizosaccharomyces pombe homolog fhn1 ( SPBC1685.13 ). We conclude that this mechanism of plasma membrane organization is conserved through the phylum Ascomycota . We used a hemagglutinin (HA)/Suc2/His4C reporter to determine the membrane topology of Nce102. In contrast to predictions, its N and C termini are oriented toward the cytosol. Deletion of the C terminus or even of its last 6 amino acids does not disturb protein trafficking, but it seriously affects the formation of MCC. We show that the C-terminal part of the Nce102 protein is necessary for localization of both Nce102 itself and Can1 to MCC and also for the formation of furrow-like membrane invaginations, the characteristic ultrastructural feature of MCC domains.

More selective interactions of nanoparticles with cells would substantially increase their potential for diagnostic and therapeutic applications. Thus, it would not only be highly desirable that nanoparticles can be addressed to any cell with high target specificity and affinity, but that we could unequivocally define whether they rest immobilized on the cell surface as a diagnostic tag, or if they are internalized to serve as a delivery vehicle for drugs. To date no class of targets is known that would allow direction of nanoparticle interactions with cells alternatively into one of these mutually exclusive events. Using MCF-7 breast cancer cells expressing the human Y 1 -receptor, we demonstrate that G protein-coupled receptors provide us with this option. We show that quantum dots carrying a surface-immobilized antagonist remain with nanomolar affinity on the cell surface, and particles carrying an agonist are internalized upon receptor binding. The receptor functions like a logic “and-gate” that grants cell access only to those particles that carry a receptor ligand “and” where the ligand is an agonist. We found that agonist- and antagonist-modified nanoparticles bind to several receptor molecules at a time. This multiligand binding leads to five orders of magnitude increased-receptor affinities, compared with free ligand, in displacement studies. More than 800 G protein-coupled receptors in humans provide us with the paramount advantage that targeting of a plethora of cells is possible, and that switching from cell recognition to cell uptake is simply a matter of nanoparticle surface modification with the appropriate choice of ligand type.