Structure of the regular surface layer of Aquaspirillum serpens MW5.

The structure of the regular surface layer of Aquaspirillum serpens MW5 has been investigated by electon microscopy supplemented by computer image processing and least-squares analysis. The layer has a ribbed appearance, both on the bacterium and in isolated, negatively stained fragments. However, detailed analysis indicated that the layer was composed of two hexagonal sheets having p6mm symmetry and a = 16 nm. One sheet was staggered by one half repeat along a (1,0) line of the p6nm lattice relative to the second so that, in projection, the pattern of the composite layer was a translational moiré, characterized by a series of ribs spaced 16 nm apart. The ribbed layer had cmm symmetry with a = 32 nm and b = 18.5 nm. Analysis of this pattern indicated that the two p6nm hexagonal sheets were unevenly stained, and this was confirmed by using least-squares methods to simulate the observed pattern by combining two hexagonal patterns. The general structure of the layer was consistent with a role as a selective and protective barrier on the cell surface.     

Three-dimensional structure of the tetragonal surface layer of Sporosarcina ureae.

The three-dimensional structure of the regular surface layer of Sporosarcina ureae has been determined to a resolution of 1.7 nm by electron microscopy and image reconstruction. The S-layer has p4 symmetry, a lattice constant of 12.9 nm, and a minimum thickness of 6.6 nm. The reconstruction reveals a distinct domain structure: a massive core, arms connecting adjacent unit cells, and spurs which make contact at the subsidiary fourfold symmetry axes. In the z-direction the domains appear to be arranged in three planes, creating two entirely different surface reliefs. The S-layer has a complex pattern of pores and gaps that are 2 to 3 nm wide. In addition, the secondary-structure composition has been determined by infrared spectroscopy: about 35% of the polypeptide appears to have a beta-structure conformation.     

The Structure and Characterization of the Surface Protein Layer of a Comamonas-Like Organism

The regular surface layer of a strain of a Comamonas-like organism was examined by electron microscopy. The surface layer protein was easily extracted from the cell surface by a 2.5 M solution of lithium chloride. The protein subunit has a molecular size of 32,000 daltons, but usually forms a large aggregate of more than 1,200,000 daltons. In the extract it formed a regular array of p4 symmetry and was observed to be intimately associated with fragments of lipopolysaccharide. The size of a subunit determined by the negative staining method and the image processing method measured 5.2 × 6.4 nm (width and length), was arranged in a cobblestone-like pattern, and was located in a lattice space measuring 13.0 nm square.     

Ultrastructural Architecture and Organization of the Spore Envelope during Development in Thelohania bracteata (Strickland, 1913) after Freeze-Etching*

An ultrastructural study was made of the spore envelope during development in the microsporidan, Thelohania bracteata. The frozen-etched outer (convex) face of the relatively thin spore coat in the earliest immature stage of development has a granular structure in regular array. The inner (concave) face bears particles as well as depressions arranged in a net-like pattern. The mature spore coat has a substructure of numerous microfibers, ～8 nm in diameter, arranged in a matrix and forming thin layers which run parallel to the spore surface. The mature spore coat possesses both outer and inner limiting layers. The outer (convex) face of the outer limiting layer is granular. The convex face of inner limiting layer bears many particles as well as many long, narrow depressions. The concave face of the inner limiting layer carries many stud-like projections, ～40 nm long and 30 nm high, which are complementary to the depressions observed on the convex face. In addition, the concave face has subunits ～15 nm in diameter, apparently arranged in a hexagonal pattern with a center to center distance of ～18 nm. The change in size of these projections, depressions, and subunits presumably is related to spore maturation.     

The tetragonal surface layer of Clostridium aceticum: three-dimensional structure and comparison with the hexagonal layer of Clostridium thermohydrosulfuricum

The regular surface layer (S-layer) of Clostridium aceticum has been isolated and the three-dimensional structure determined to a resolution of 2.0 nm from tilt series of negatively stained preparations. It has tetragonal symmetry with a lattice constant of 12 nm and a thickness of 6 nm; there are probably 4 protein monomers per unit cell. A large proportion of the protein is concentrated in massive "cores" at the major four-fold axes which are situated towards the inner surface of the layer. From these cores, delicate arms extend towards the minor four-fold axes, where secondary connectivity is established near the exterior surface. When viewed from the outside, each of the cores appears to have a large central depression, rather than a true "pore". Since this general pattern of mass distribution is shared by the hexagonal S-layer of Clostridium thermohydrosulfuricum, some consideration has been given to the possible evolutionary steps leading to changes in symmetry. From modelling experiments, it is evident that the change from four-fold to six-fold symmetry in this instance could be accomplished simply by the loss of a structural "domain" from the protomer.     

Three-dimensional structure of the T-layer of Bacillus sphaericus P-1.

The three-dimensional structure of the regular surface layer of Bacillus sphaericus P-1 (T-layer) was determined to a resolution of ca. 2.5 nm by electron microscopy and image analysis. The T-layer has P4 symmetry, a lattice constant of 13 +/- 0.2 nm, and a thickness of ca. 8 nm. The reconstruction revealed three distinct domains: a major, a minor, and an arm domain. In the z-direction, the domains are arranged in two planes creating two different surface reliefs.     

Three-dimensional structure of the regular surface layer (HPI layer) of Deinococcus radiodurans

The low-resolution structure of the regular surface layer of Deinococcus radiodurans has been determined from negatively stained specimens by three-dimensional electron microscopy. The layer has P6 symmetry, a lattice constant of 18 nm and a thickness of 6.5 nm. Three-dimensional reconstruction was performed by a hybrid real space/Fourier space approach that incorporates partial compensation of lattice distortions: The model obtained is discussed in the light of independent information about the surface structure of this layer, derived from metal shadowing and surface relief reconstruction. While agreement is quite satisfactory for the apparently more rigid inner surface, the outer surface shows severe flattening effects. The structure of the HPI layer is compared with other bacterial surface layers using a classification scheme that is outlined in the Appendix.     

Electron Microscopic Study of Membranes and Walls of Bacteria and Changes Occurring During Growth Initiation

Thin sections of stationary-phase Streptococcus lactis cells showed that the wall and membrane are 20 and 7 nm thick, respectively. Whole cells were examined by negative staining with ammonium molybdate and by shadowing. On air-drying of whole cells, the membrane pulled away from the wall revealing adhesions between these organelles. Adhesions could not be seen after subculture of the stationary-phase cells into complex media or into solutions containing glucose, KCl, and CaCl(2) in tris(hydroxymethyl)aminomethane buffer. The adhesions were also observed in stationary-phase cells of other gram-positive bacteria. Fractured freeze-etched cells of S. lactis had a smooth outside surface, but the inside of the wall (or outside of the membrane) had a regular structure, repeating at 10 nm, which could correspond to the adhesions observed in the negatively stained air-dried cells. Freeze-etching also revealed holes in the outside wall which had the shape of inverted truncated cones. The outside diameter of the cone was 60 nm, and the diameter on the inside surface of the wall was 20 nm. The membrane had upstanding plugs, 20 nm in diameter, which could fill the holes in the wall.     

The cell envelope of Thermoproteus tenax: three-dimensional structure of the surface layer and its role in shape maintenance

The sulphur-dependent archaebacterium Thermoproteus tenax has a cylindrical cell shape variable in length, but constant in diameter. Its whole surface is covered by a regular protein layer (S-layer). The lattice has p6 symmetry and a lattice constant of 32.8 nm. The three-dimensional reconstruction from a tilt series of isolated and negatively stained S-layer shows a complex mass distribution of the protein: a prominent, pillar-shaped protrusion is located at the 6-fold crystallographic axis with radiating arms connecting neighbouring hexamers in the vicinity of the 3-fold axis. The base vectors of the S-layer lattice have a preferred orientation with respect to the longitudinal axis of the cell. The layer can be seen as a helical structure consisting of a right-handed, two-stranded helix, with the individual chains running parallel. Supposing that new S-layer protein is inserted at lattice faults (wedge disclinations) near the poles, growing of the layer would then proceed by moving a disclination at the end of the helix. The constant shape of the cell, as well as the particular structure of the layer, strongly suggest that this S-layer has a shape-maintaining function.     

Three-dimensional structure of a regular surface layer from Pseudomonas acidovorans

The regular surface layer of Pseudomonas acidovorans was investigated by computer processing of a series of tilted view electron micrographs, and a reconstruction of the three-dimensional structure was obtained. The pattern is tetragonal and consists of massive identical subunits, block-like in face-view, which interlock loosely in a simple cobblestone pattern. The square unit cell has a lattice constant of 11 nm. The surface layer pattern of P. acidovorans appears to be more dependent on the underlying membrane for maintaining its integrity than those so far studied in other bacteria.     

Ultrastructure and partial characterization of a regular array in the cell wall of Lactobacillus brevis.

The cell wall of Lactobacillus brevis was revealed by electron microscopy to have an outer layer composed of a regular array. The morphological unit of the regular array appeared to consist of four spherical subunits, each about 2 nm in diameter, which were arranged in a tetragonal pattern about 4.5 by 7.0 nm in dimension. The regular array was composed of the tetragonal units in rows in two directions at an angle of about 75 degrees to each other. The average spacing between the rows was about 10 nm in one direction and about 7 nm in the other. The tetragonally arranged subunits were removed from the cell wall by treatment with guanidine hydrochloride, urea, or sodium dodecyl sulfate (SDS) but not by the action of ethylenediaminetetraacetate, nonionic detergents, or proteolytic enzymes except pepsin. The regular subunits were shown to be composed of a protein with a molecular weight of about 51,000 by SDS-polyacrylamide gel electrophoresis.     

Three-dimensional structure of the regularly constructed surface layer from Synechocystis sp. strain CLII

The isolated, outermost cell wall layer from Synechocystis sp. strain CLII is described using electron microscopy and Fourier reconstruction to study the three-dimensional structure of the proteins within the layer to a resolution of ca. 3 nm. This surface layer forms regular hexagonal arrays (a = b = 15.2 nm). The two-dimensional space group is p6. The monomer proteins form hexamers arranged around a central hollow cylinder. The linkers between the hexamers are of the delta type and are located approximately in the central section between the top and bottom of the protein layer.     

Three-dimensional structure of an open form of the surface layer from the fish pathogen Aeromonas salmonicida.

Cell-free culture supernatants of a lipopolysaccharide (LPS) O-polysaccharide-deficient, single-insertion transposon mutant of the tetragonal surface protein array (S layer)-containing fish pathogen Aeromonas salmonicida were examined by electron microscopy. Negative staining showed that the S layer was released as sheets of tetragonal material, indicating that although surface retention of assembled S layer requires the presence of wild-type LPS oligosaccharides, initial assembly of S-layer subunits into sheets does not require the presence of O-polysaccharide chains. The three-dimensional structure of the S layer was reconstructed from tilted micrographs of the released sheets. Horizontal sections through this reconstruction showed that the released sheets were composed of two identical S layers that were perfectly in register. The reconstructed layer had a lattice constant of 12.5 nm. At a resolution of 1.6 nm, the layer consisted of a major tetragon at one fourfold axis of symmetry and a minor tetragon at the second fourfold axis of symmetry. The core, composed of four of the major domains, contained a large depression and was located toward the inside of the layer. The minor tetragon provided connectivity within the layer and was located toward the outer surface of the layer. Projections through the double layer gave a type I (closed) pattern (M. Stewart, T. J. Beveridge, and T. J. Trust, J. Bacteriol. 166:120-127, 1986), yet projections through the single layer indicated that the type II (open) pattern was present. This open pattern was indistinguishable from that seen in S layer released from the surfaces of wild-type cells.     

Regular Array in the Cell Wall of Lactobacillus fermenti as Revealed by Freeze-Etching and Negative Staining1

Freeze-etching of Lactobacillus fermenti F-4 (NCTC 7230) revealed that the outer layer of the cell wall was composed of a regular array in which parallel lines ran obliquely to the longitudinal axis of the cell with an average distance between the centers of about 9.6 nm and were intersected by thinner lines with an average periodicity of approximately 6.2 nm at an angle of about 75°. Occasionally the direction of the striation was discontinuously shifted near one end of the cell. Beneath the regular array the middle cell wall layer packed with granules and the smooth inner cell wall layer were discernible and the mesosomes were also visible in the cytoplasm. When the ultrastructure of isolated outer cell wall fragments was examined by negative staining, the regular array appeared to be composed of subunits, about 3.6 nm in diameter, which were arranged in a tetragonal pattern. The tetragonal array consisted of the subunits in rows in two directions at an angle of about 75° to each other. The average spacing between the rows was about 9.3 nm in one direction and 5.5 nm in the other direction.     

The three-dimensional structure of reovirus obtained by cryo-electron microscopy.

The structures of reovirus serotypes T2J (Jones), T3D (Dearing) and the T3D core particle have been determined by cryo-electron microscopy and image processing. At a resolution of 30 A the two serotypes have similar features. The core is visible within the virus structure. The outer surface of the virus particles contains 120 holes at T = 13.1 local 6-fold axes. The holes penetrate into the virus as far as the surface of the internal core shell. Protrusions extending 4 nm from the virus surface surround each hole on the outside of the virus. At the 5-fold axes on the surface of the virus flat 'penton craters' form covers over the underlying core spikes. The detailed structure of the reovirus shell is very different to that of rotavirus although both have holes at T = 13.1 axes. Little evidence was seen of reovirus fibres extending from the virus surface.     

A Polarization Filter Based on Photonic Crystal Fiber with Asymmetry Around Gold-Coated Holes

We propose a modified design for a photonic crystal fiber (PCF) filter based on surface plasmon resonance(SPR). The air holes are arrayed in rectangular lattices, while the size and the pitches of holes around the gold-coated holes are different. That can separate the x-polarization and y-polarization of second-order surface plasmon polariton (SPP). The resonance strength of the surface plasmon mode and import of structural parameters of the PCF on the filter characteristics are studied through using the finite element method (FEM). Numerical simulations demonstrate that the thickness of the gold layer, the gold-coated or gold-filled, and the asymmetry around the gold-coated holes have a great effect on the filter characteristics. It is certain to obtain a resonance strength as high as 873 and 771.5 dB/cm at the communication wavelength of 1050 and 1310 nm in x-polarization by adjusting the size and the place of the gold-coated holes, while the loss is extremely low in y-polarization.     

Outer membrane-bound protease of Deinococcus radiodurans

The regular surface layers (S-layers) of two Deinococcus radiodurans strains R1 and Sark, undergo limited proteolysis during preparation. This is due to cellular proteases that create strain-specific polypeptide patterns in SDS-PAGE. Proteolytic activity was detected in both vesicles of the outer membrane, as well as in the culture supernatant from both strains. The protease of the strain R1 was purified to homogeneity and characterized; it has been classified as a serine protease. The enzyme of strain Sark proved to be almost identical to the R1-protease with respect to both the molecular and the catalytic properties. Treatment of the regular surface layer proteins from both strains with the purified R1-protease revealed the strain-specific SDS-polypeptide patterns, indicating differences in the primary structure of the two proteins.     

Superficial Macromolecular Arrays on the Cell Wall of Spirillum putridiconchylium

Electron microscopy of the cell envelope of Spirillum putridiconchylium, using negatively stained, thin-sectioned, and replicated freeze-etched preparations, showed two superficial wall layers forming a complex macromolecular pattern on the external surface. The outer structured layer was a linear array of particles overlying an inner tetragonal array of larger subunits. They were associated in a very regular fashion, and the complex was bonded to the outer, pitted surface of the lipopolysaccharide tripartite layer of the cell wall. The relationship of the components of the two structured layers was resolved with the aid of optical diffraction, combined with image filtering and reconstruction and linear and rotary integration techniques. The outer structural layer consisted of spherical 1.5-nm units set in double lines determined by the size and arrangement of 6- by 3-nm inner structural layer subunits, which bore one outer structural layer unit on each outer corner. The total effect of this arrangement was a double-ridged linear structure that was evident in surface replicas and negatively stained fragments of the whole wall. The packing of these units was not square but skewed by 2 degrees off the perpendicular so that the "unit array" described by optical diffraction and linear integration appeared to be a deformed tetragon. The verity of the model was checked by using a photographically reduced image to produce an optical diffraction pattern for comparison with that of the actual layers. The correspondence was nearly perfect.     

Scanning electron microscopy of changes in epidermal structure occurring during the shedding cycle in squamate reptiles

Previous studies of squamate epidermal structure have focused on either histology and ultrastructure or oberhautchen surface texture as revealed by scanning electron microscopy (SEM). Using SEM data drawn from a variety of lizard taxa (primarily iguanids, but also agamids, chamaeleonids, and scincids), as well as amphisbaenians and colubrid snakes, we relate the surfaces encountered in gross dissection of squamate skin to histologically identifiable layers, and characterize their surface structure. Only the oberhautchen bears the repeating pattern of ornamentation noted by previous authors. Because the clear layer is a perfect template of the oberhautchen surface, it is the only layer with which the oberhautchen might be confused. However, the clear layer can be identified by its tendency to curl and crack during preparation. All other surfaces encountered were relatively featureless, except for impressions left by dermal “papillae” associated with mechanoreceptors. Using a method for examining preserved specimens to determine the stage in the shedding cycle, we assess two sources of variation in epidermal surface structure: stage in the shedding cycle and wear. Examination of immature renewal-phase epidermis suggests that the oberhautchen does not mature synchronously across a single scale or across body regions. Comparing inner- and outer-generation oberhautchen in sheddingphase epidermis, we conclude that changes in surface appearance caused by natural wear fall into two categories: discrete scratches and accumulation of debris. We see no evidence of overall “buffing” on a microscopic level, though surface structure may be obscured by scratches and gouges. Many squamate taxa show a gradient from low relief surface structure on elevated regions such as keels to high relief patterns at scale edges. This gradient is not due to wear; its significance is unknown.     

Streptavidin crystals as nanostructured supports and image-calibration references for cryo-EM data collection

For cryo-EM structural studies, we seek to image membrane proteins as single particles embedded in proteoliposomes. One technical difficulty has been the low density of liposomes that can be trapped in the approximately 100nm ice layer that spans holes in the perforated carbon support film of EM grids. Inspired by the use of two-dimensional (2D) streptavidin crystals as an affinity surface for biotinylated DNA (Crucifix et al., 2004), we propose to use the crystals to tether liposomes doped with biotinylated lipids. The 2D crystal image also serves as a calibration of the image formation process, providing an absolute conversion from electrostatic potentials in the specimen to the EM image intensity, and serving as a quality control of acquired cryo-EM images. We were able to grow streptavidin crystals covering more than 90% of the holes in an EM grid, and which remained stable even under negative stain. The liposome density in the resulting cryo-EM sample was uniform and high due to the high-affinity binding of biotin to streptavidin. Using computational methods, the 2D crystal background can be removed from images without noticeable effect on image properties.