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PubMed2003

Viral internal ribosome entry site structures segregate into two distinct morphologies.

An increasing number of viruses have been shown to initiate protein synthesis by a cap-independent mechanism involving internal ribosome entry sites (IRESs). Predictions of the folding patterns of these RNA motifs have been based primarily on sequence and biochemical analyses. Biophysical confirmation of the models has been achieved only for the IRES of hepatitis C virus (HCV), which adopts an open structure consisting of two major stems. We have conducted an extensive comparison of flavivirus and picornavirus IRES elements by negative stain transmission electron microscopy. All of the flavivirus IRESs we examined (those of GB virus-B, GB virus-C, and classical swine fever virus) fold to give a structure similar to that of the HCV IRES, as does an IRES recently found on mRNA encoded by human herpesvirus 8. The larger picornavirus IRESs (those of foot-and-mouth disease virus, rhinovirus, encephalomyocarditis virus, and hepatitis A virus) are morphologically similar, comprising a backbone with two protruding stems, and distinct from the flavivirus IRESs.

Animals↗

PubMed1992

A support film of plasma-polymerized naphthalene for electron microscopy: method of preparation and application.

Methods of preparing of a new support film by plasma polymerization in a glow discharge, and its application were described. The recently developed plasma polymerization replica technique was used to prepare ultrathin films from naphthalene monomer gas on the surface of a newly cleaved sodium chloride crystal or on cover glass. The film was floated off on water or hydrofluoric acid solution to free it from the base. The plasma-polymerized naphthalene support film (PNS) prepared in this way was shown to have excellent properties by its application to negative staining of virus antigen particles and by the observation of whole ultrathin sections of animal tissue mounted on a 2 x 1 mm single slot grid. Features of the new support film are (1) its ease of preparation as a clean, very thin film of less than 10 nm, (2) its amorphous texture and high transparency to electrons, (3) its mechanical strength, resistance to heat and chemicals, and electron bombardment, and (4) its smooth and slightly hydrophilic surface. The PNS would be useful for both routine and high-resolution electron microscopy.

Animals↗

PubMed1998

Imaging two-dimensional arrays of soluble proteins by atomic force microscopy in contact mode using a sharp supertip.

A sharp tip with high aspect ratio is required for imaging biological macromolecules by atomic force microscopy (AFM). A tip with the end radius of curvature less than 3 nm has been reproducibly fabricated by means of electron beam deposition (EBD) in a field-emission scanning electron microscope. Two-dimensional protein arrays of ferritin and catalase, prepared at air/water interface and transferred onto silicon wafer, could be imaged both in air and in water by AFM using this sharp EBD-tip in contact mode. The negative staining preparation conventionally used in the transmission electron microscopy of protein was applied and shown to be quite effective in fixing the protein arrays for the AFM imaging in air. Individual molecules of ferritin and catalase were visible in the two-dimensional arrays. Also, imaging in water of these protein arrays presented molecular images clearer than in air, due probably to the absence of the adhesion force and the resulting weak lateral force during scanning. These images convince us of the capability of this supertip for AFM studies of biological molecules under aqueous conditions.

Air↗

PubMed2006

The three-dimensional arcitecture of the EJC core.

The exon junction complex (EJC) is a macromolecular complex deposited at splice junctions on mRNAs as a consequence of splicing. At the core of the EJC are four proteins: eIF4AIII, a member of the DExH/D-box family of NTP-dependent RNA binding proteins, Y14, Magoh, and MLN51. These proteins form a stable heterotetramer that remains bound to the mRNA throughout many different cellular environments. We have determined the three-dimensional (3D) structure of this EJC core using negative-stain random-conical tilt electron microscopy. This structure represents the first structure of a DExH/D-box protein in complex with its binding partners. The EJC core is a four-lobed complex with a central channel and dimensions consistent with its known RNA footprint of about ten nucleotides. Using known X-ray crystallographic structures and a model of three of the four components, we propose a model for complex assembly on RNA and explain how Y14:Magoh may influence eIF4AIII's RNA binding.

Crystallography, X-Ray↗

PubMed1991

The glucocorticoid receptor in homodimeric and monomeric form visualised by electron microscopy.

The purified glucocorticoid receptor (GR) from rat liver has been visualised by electron microscopy. The specimens were prepared by spreading on thin carbon support and negatively stained using uranyl acetate. Two forms of GR, the monomeric and the dimeric forms, were identified based on size, chromatographic distribution, and DNA binding properties. The GR monomer consists of two globular domains of slightly different size with a thinner connecting domain in between. In the absence of DNA the dimeric GR has a characteristic four-leaf clover structure. The size and appearance of this structure is consistent with two GR subunits arranged in a side-by-side fashion. Monomeric and dimeric GR specifically bound to DNA are also shown.

Animals↗

PubMed1995

Subunit organisation and symmetry of pore-forming, oligomeric pneumolysin.

We present a detailed analysis of the oligomeric subunit organisation of pneumolysin by the use of negative stain electron microscopy and image processing to produce a projection density map. Analysis of the rotational symmetry has revealed a large and variable subunit number, between 40-50. The projected subunit density by rotational averaging shows at least two distinct subunit domains at different radial positions. Side views of the rings reveal further details concerning the dimensions of the oligomer in the membrane. On the basis of these observations and our previous knowledge of the monomer domain structure we propose that the 4-domain subunits are packed in a square planar arrangement to form the pneumolysin oligomer.

Bacterial Proteins↗

PubMed1993

Le(y) antigen expression is correlated with apoptosis (programmed cell death).

Apoptosis (programmed cell death) is a basic physiological process which determines specific patterns of tissue size and shape, and balance of cell number, during morphogenesis, and seems to play an integral role in oncogenic progression. Since dramatic changes of cellular glycosylation pattern are well known to be closely correlated with differentiation, development and oncogenesis, it is likely that similar specific changes are associated with apoptosis. However, this possibility has not been systematically investigated. We therefore carried out histological studies of many tumours and normal tissues for which a high incidence of apoptosis is believed to occur. Sections were stained with monoclonal antibodies (MoAbs) directed to carbohydrate antigens Le(y) and Le(x), proliferating cellular nuclear antigen (PCNA) and Fas (previously claimed to be an apoptosis-inducing antigen). Antibody staining patterns were compared with morphological cell characteristics as revealed by haematoxylin/eosin staining, and DNA fragmentation patterns (a marker of apoptosis) as revealed by 3'-OH nick-end labelling technique. We found that expression of Le(y) (defined by MoAb BM1) is closely correlated with the process of apoptosis, but not with cell proliferation or necrosis. Within Le(y)-positive areas of tissue sections, typical apoptotic morphological changes and DNA fragmentation (as revealed by positive nick-end labelling) were frequently observed in certain loci, although not all Le(y)-positive cells showed such signs of apoptosis. Le(y)-positive areas showed consistent negative staining by MoAb directed to PCNA and negative or weak staining by MoAb directed to Fas antigen, regardless of tissue source. No such trends were observed for Le(x) glycosylation. We conclude that Le(y) expression is a useful phenotypic marker predictive of apoptosis, i.e. some (although not all) Le(y)-positive cells subsequently become apoptotic.

Antibodies, Monoclonal↗

PubMedDate not supplied

New rapid staining methods of Cryptosporidium oocysts in stools.

Two new extemporaneous negative-staining methods are proposed to detect Cryptosporidium oocysts in stools, using light-green and merbromine in 1% and 2% aqueous solution, respectively. A Ziehl-Neelsen stain as modified by Henriksen and Polhenz was used as a reference technique. A comparison between these two new stains and the reference, a modified Ziehl-Neelsen mod. method gave almost identical sensitivity and specificity. We propose their use in routine diagnosis for enteric cryptosporidiosis.

Acquired Immunodeficiency Syndrome↗

PubMed2002

Structural analysis and evidence for dynamic emergence of Bacillus anthracis S-layer networks.

Surface layers (S-layers), which form the outermost layers of many Bacteria and Archaea, consist of protein molecules arranged in two-dimensional crystalline arrays. Bacillus anthracis, a gram-positive, spore-forming bacterium, responsible for anthrax, synthesizes two abundant surface proteins: Sap and EA1. Regulatory studies showed that EA1 and Sap appear sequentially at the surface of the parental strain. Sap and EA1 can form arrays. The structural parameters of S-layers from mutant strains (EA1(-) and Sap(-)) were determined by computer image processing of electron micrographs of negatively stained regular S-layer fragments or deflated whole bacteria. Sap and EA1 projection maps were calculated on a p1 symmetry basis. The unit cell parameters of EA1 were a = 69 A, b = 83 A, and gamma = 106 degrees, while those of Sap were a = 184 A, b = 81 A, and gamma = 84 degrees. Freeze-etching experiments and the analysis of the peripheral regions of the cell suggested that the two S-layers have different settings. We characterized the settings of each network at different growth phases. Our data indicated that the scattered emergence of EA1 destabilizes the Sap S-layer.

Bacillus anthracis↗

PubMed1991

Ultrastructure of chromatin. II. Three-dimensional reconstruction of isolated fibers.

Electron-microscope tomography has been used to reconstruct isolated, negatively stained chromatin fibers from Necturus maculosus erythrocytes. Tilt series micrographs from +70 degrees to -70 degrees at 5 degrees intervals were obtained, allowing a reconstruction resolution of 3.3 nm for fibers lying parallel to the tilt axis. The fibers were found to be flattened in the plane of the carbon support, and also stained differentially according to the distance from the carbon. A number of methods of presenting the three-dimensional information were explored. Especially useful was an automatic peak search method for locating putative nucleosome positions coupled with the production of a computer-generated model. Other valuable techniques included the generation of projection stereograms and construction of solid models. A peripheral location of nucleosomes in the chromatin fiber was indicated, and helical arrangements of nucleosomes were observed over short regions. However, no long-range ordering of nucleosomes was apparent. The extent to which this lack of order may be the result of events occurring during the preparation of chromatin for electron microscopy is discussed.

Animals↗

PubMedDate not supplied

Three-dimensional structure of Bordetella pertussis fimbriae.

We describe the helical structure of Bordetella pertussis fimbriae of serotype 3/6 as determined to a resolution of approximately 2.5 nm by three-dimensional reconstruction of negatively stained electron micrographs. The fimbria has a distinctly polar structure whose axial repeat of 13 nm contains five copies of the fim3 gene product (22 kDa) in two complete turns. These subunits are connected by interactions along the fimbrial backbone which, unlike other classes of bacterial fimbriae, has no axial channel. Its outer diameter is approximately 5.7 nm, and the most pronounced feature is a radially protruding domain that gives the fimbria its characteristic serrated appearance. Serotype 2 fimbriae, composed of the fim2 subunit which is 60% homologous with fim3, have essentially the same quaternary structure. These observations are discussed in relation to fimbrial phase variation and structure-based classification of fimbriae/pili.

Antigens, Bacterial↗

PubMed1996

Fine surface structure of enterotoxemic Escherichia coli O139:K12 strains associated with swine edema disease.

The fine structure of the cell surface of seven enterotoxemic Escherichia coli (ETEEC) O139:K12 strains isolated from piglets with edema disease were examined electron microscopically using both the negative-staining method and the freeze-substitution fixation method. Densely packed, fine fibers were observed; they consisted of a capsule layer approximately 25 nm thick around the cell surfaces of strains 107/86, IW-2, ED-3, ED-43, and ED-61, all of which have a capacity to adhere strongly to HEp-2 cells. In contrast, no such structure was observed on the surface of strains RK-O139 or ED-1, both of which adhere only weakly to HEp-2 cells. These results suggest that the capsule structure might be associated with the ability to adhere to HEp-2 cells and, as a result, also potentially play some role in ETEEC infection.

Animals↗

PubMed1994

Nephrotic tunnels in glomerular basement membrane as revealed by a new electron microscopic method.

To clarify the ultrastructure in situ of the normal human glomerular basement membrane and ultrastructural changes of the glomerular basement membrane in patients with nephrotic syndrome, specimens of normal renal tissue and specimens from patients with membranous nephropathy, lupus nephritis, minimal change nephrotic syndrome, diabetic nephropathy, and Alport's syndrome were obtained. Specimens were examined by transmission electron microscopy by the newly devised "tissue negative staining method." Normal glomerular basement membrane showed a three-dimensional lattice-like meshwork of fibrils measuring 1.9 +/- 0.4 nm in diameter that formed numerous uniform, round, oval, or polygonal pores 2.5 +/- 0.4 nm in short diameter and 2.8 +/- 0.5 nm in long dimension. The nephrotic glomerular basement membrane revealed varying degrees of ultrastructural defects, the most prominent being tunnels and cavities. Tortuous tunnels measuring approximately 15 to 50 nm in diameter penetrated the entire glomerular basement membrane. Cavities of various shapes measuring 15 to 200 nm in diameter were diffusely scattered in the glomerular basement membrane and occasionally aggregated to form a honeycomb structure that occupied the whole thickness of the glomerular basement membrane. These defects appeared to be the pathway for protein leakage.

Diabetic Nephropathies↗

PubMed1993

Characterization of the cell wall of the sheathed methanogen Methanospirillum hungatei GP1 as an S layer.

The cell wall of Methanospirillum hungatei GP1 is a labile structure that has been difficult to isolate and characterize because the cells which it encases are contained within a sheath. Cell-sized fragments, 560 nm wide by several micrometers long, of cell wall were extracted by a novel method involving the gradual drying of the filaments in 2% (wt/vol) sodium dodecyl sulfate and 10% (wt/vol) sucrose in 50 mM N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) buffer containing 10 mM EDTA. The surface was a hexagonal array (a = b = 15.1 nm) possessing a helical superstructure with a ca. 2.5 degrees pitch angle. In shadowed relief, the smooth outer face was punctuated with deep pits, whereas the inner face was relatively featureless. Computer-based two-dimensional reconstructed views of the negatively stained layer demonstrated 4.0- and 2.0-nm-wide electron-dense regions on opposite sides of the layer likely corresponding to the openings of funnel-shaped channels. The face featuring the larger openings best corresponds to the outer face of the layer. The smaller opening was encircled by a stalk-like mass from which 2.2-nm-wide protrusions were resolved. The cell wall in situ was degraded at pH 9.6 at 56 degrees C but was unaffected at pH 7.4 at the same temperature. The cell wall was composed of two nonglycosylated polypeptides (114 and 110 kDa). The cell wall resembled an archaeal S layer and may function in regulating the passage of small (< 10-kDa) sheath precursor proteins.

Bacterial Proteins↗

PubMed1994

Structural specialization in the flagellum of the spermatozoon of the bloodsucking bug (Rhodnius prolixus; Hemiptera, Reduviidae).

Spermatozoa of the triatomideo Rhodnius prolixus possess an axoneme with a 9 + 9 + 2 microtubule pattern and two mitochondrial derivatives. Bridges occur between axoneme and mitochondrial derivatives. Two paracrystalline structures embedded in amorphous regions were observed in the mitochondrial derivative. The use of the negative staining technique shows a zig-zag profile in the mitochondrial derivatives due to infolding to the cristae, regularly spaced with approximately 50 nm. This spacing is also observed in the distribution of the strands of particles in the mitochondrial membrana as seen in freeze-fracture replicas. In the P-fracture face of the flagellar plasma membrane, a regular array of the intramembranous particles was observed. This array consists of two rows, with 12-15 particles, and occurs in the space between the mitochondrial derivatives. Thus R. prolixus spermatozoon present a membrane domain, localized in the flagellar region, and bridges between mitochondrial membrane derivatives and the plasma membrane are probably attached to the flagellar components. These membrane specializations may be related to the production of co-ordinated flagellar movement, and can contribute significantly to further phylogenetic studies.

Animals↗

PubMed2001

Analysis of the PilQ secretin from Neisseria meningitidis by transmission electron microscopy reveals a dodecameric quaternary structure.

PilQ is a member of the secretin family of outer membrane proteins and is specifically involved in secretion of type IV pili in Neisseria meningitidis, Neisseria gonorrhoeae, and Pseudomonas aeruginosa. The quaternary structure of PilQ from N. meningitidis was analyzed by transmission electron microscopy by using a negative stain. Single particle averaging was carried out with a total data set of 650 individual particles, which produced a projection map generated from 296 particles at an estimated resolution of 2.6 nm. Oligomeric PilQ adopts a donut-like structure with an external ring that is 16.5 nm in diameter surrounding a central cavity that is 6.5 nm in diameter. Self-rotation and power spectrum analysis demonstrated the presence of 12-fold rotational symmetry, showing that PilQ is organized as a ring of 12 identical subunits. A model of the type IV meningococcal pilus fiber, based on the X-ray crystal structure of the N. gonorrhoeae pilin subunit, fitted neatly into the cavity, demonstrating how PilQ could serve as a channel for the growing pilus fiber.

Bacterial Outer Membrane Proteins↗

PubMedDate not supplied

Electron microscopy of Bacillus subtilis GroESL chaperonin and interaction with the bacteriophage phi 29 head-tail connector.

The Bacillus subtilis GroESL chaperonin was isolated by sucrose density gradient centrifugation and the constituent GroES and GroEL moieties were purified by electrophoresis in agarose. Electron microscopic images of negatively stained GroEL and GroES oligomers and GroESL complexes were averaged using a reference-free alignment method. The GroEL and GroES particles had the sevenfold symmetry characteristic of their Escherichia coli counterparts. GroESL complexes, reconstituted efficiently in vitro from GroEL and GroES in the absence of added ADP or ATP, had the characteristic bullet- and football-like shapes in side view. Purified bacteriophage phi 29 head-tail connectors having a mass in excess of 0.4 MDa were shown to bind to GroESL at the end opposite to the GroES. The same GroESL-connector complexes were isolated from phage-infected cells in which capsid assembly was blocked, and thus the complex may have functional significance in phi 29 morphogenesis.

Bacillus Phages↗

PubMed1984

Ultrastructural study of adhesion of enterotoxigenic Escherichia coli to erythrocytes and human intestinal epithelial cells.

The adhesion to erythrocytes and human intestinal epithelial cells of enterotoxigenic Escherichia coli strains H10407, B2C, and H10407P, expressing colonization factor antigen I (CFA/I), CFA/II, and type 1 fimbriae, respectively, was examined by electron microscopy. CFA and type 1 fimbriae were visualized by negative staining in thin sections after en bloc staining with ruthenium red and by immune labeling with antisera raised against purified fimbriae. By negative and ruthenium red staining, CFA/I, CFA/II, and type 1 fimbriae were indistinguishable and appeared as approximately 7-nm-diameter hollow cylindrical structures up to 1.5 micron in length; strain B2C also produced 2- to 3-nm-diameter flexible fibrillar fimbriae. Bacteria producing CFA/I, CFA/II, and type 1 fimbriae adhered to and agglutinated human, bovine, and guinea pig erythrocytes, respectively; CFA/I and CFA/II also mediated attachment of bacteria to the brush border of isolated human duodenal enterocytes. Electron microscopy of agglutinated erythrocytes and enterocytes with adherent bacteria showed, in each case, that bacterial adhesion involved the formation of many interactions between the tips of fimbriae and receptors on the erythrocyte or enterocyte brush border membrane. Immune labeling allowed different fimbrial antigens mediating bacterial attachment to human enterocytes to be identified.

Animals↗