The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin

The diameters of chromatin fibers from Thyone briareus (sea cucumber) sperm (DNA linker length, n = 87 bp) and Necturus maculosus (mudpuppy) erythrocytes (n = 48 bp) were investigated. Soluble fibers were frozen into vitrified aqueous solutions of physiological ionic strength (124 mM), imaged by cryo-EM, and measured interactively using quantitative computer image-processing techniques. Frozen-hydrated Thyone and Necturus fibers had significantly different mean diameters of 43.5 nm (SD = 4.2 nm; SEM = 0.61 nm) and 32.0 nm (SD = 3.0 nm; SEM = 0.36 nm), respectively. Evaluation of previously published EM data shows that the diameters of chromatin from a large number of sources are proportional to linker length. In addition, the inherent variability in fiber diameter suggests a relationship between fiber structure and the heterogeneity of linker length. The cryo-EM data were in quantitative agreement with space-filling double-helical crossed-linker models of Thyone and Necturus chromatin. The data, however, do not support solenoid or twisted-ribbon models for chromatin that specify a constant 30 nm diameter. To reconcile the concept of solenoidal packing with the data, we propose a variable-diameter solid-solenoid model with a fiber diameter that increases with linker length. In principle, each of the variable diameter models for chromatin can be reconciled with local variations in linker length.     

Formation of amyloid fibrils via longitudinal growth of oligomers

Mature amyloid fibrils are believed to be formed by the lateral association of discrete structural units designated as protofibrils, but this lateral association of protofibrils has never been directly observed. We have recently characterized a thioesterase from Alcaligenes faecalis, which was shown to exist as homomeric oligomers with an average diameter of 21.6 nm consisting of 22 kDa subunits in predominantly beta-sheet structure. In this study, we have shown that upon incubation in a 75% ethanol solution, the oligomeric particles of protein were transformed into amyloid-like fibrils. TEM pictures obtained at various stages during fibril growth helped us to understand to a certain extent the early events in the fibrillization process. When incubated in 75% ethanol, oligomeric particles of protein grew to approximately 35-40 nm in diameter before fusion. Fusion of two oligomers of 35-40 nm resulted in the formation of a fibril. Fibril formation was accompanied by a reduction in the diameter of the particle to approximately 20-25 nm along with concomitant elongation to approximately 110 nm, indicating reorganization and strengthening of the structure. The elongation process continued by sequential addition of oligomeric units to give fibers 500-1000 nm in length with a further reduction in diameter to 17-20 nm. Further elongation resulted in the formation of fibers that were more than 4000 nm in length; the diameter, however, remained constant at 17-20 nm. These data clearly show that the mature fibrils have assembled via longitudinal growth of oligomers and not via lateral association of protofibrils.     

Electron microscopic visualization of RecA-DNA filaments: Evidence for a cyclic extension of duplex DNA

As visualized by electron microscopy, RecA protein binds in a highly cooperative manner to single-stranded fd DNA in solutions of 0.01 M Tris (pH 7.5). The resulting nucleoprotein filament loops are 1.25 μm in length, have a fiber diameter of 12 nm and show an indication of a 4.5 nm repeat along the axis of the compact fibers. RecA binds to linear duplex fd DNA in solutions of 0.01 M Tris (pH 7.5) to yield chains of beads which, in the presence of Mg²⁺ and ATP, coalesce into smooth filaments with a length of 1.9 μm (the length of protein-free fd duplex DNA) and have a fiber diameter of 12 nm. In solutions containing Mg²⁺ and ATP-γ-S, however, RecA binds to duplex DNA in a highly cooperative manner to yield rigid filaments 3.0 μm in length. These filaments are 12 nm in diameter and show a very clear 7.5 nm axial repeat. This extension of DNA to 150% of its usual length in the apparent absence of any single-stranded components suggests that the DNA helix must also be highly unwound and provides new insights into the mode of RecA action.     

Morphology of the Nucleoprotein Component of Rabies Virus

The intracytoplasmic ground substance, or matrix, associated with the development of rabies virus and the nucleocapsid of the virus were investigated. The filaments of the matrix were identified as virus-specific by means of ferritin-labeled antibodies. In thin sections, the diameter was 15 nm and the strands seemed to be incorporated into virions during morphogenesis of the virus. The nucleocapsid was isolated from purified virus preparations and was studied in negative contrast. The rabies nucleocapsid appeared as a single-stranded helix with a diameter of 16 nm and a periodicity of 7.5 nm; its length was in excess of 1 mum.     

LC2 involvement in the assembly of skeletal myosin filaments

The assembly of LC2-deficient myosin was studied under conditions where control and LC2-reassociated myosin assemble around the native length of about 1.5 microns. The aim of this work was to determine how loss of LC2 affects the assembly characteristics. The findings of this study can be summarized as follows: (a) LC2-deficient myosin assembles into two populations of filaments, one around 0.5 micron in length and the other around 1 micron in length. This suggests that loss of the LC2 perturbs the length-determining mechanism. (b) The population of filaments around 0.5 micron has a diameter around 14 nm and that around 1 micron a diameter around 22 nm. Neither diameter corresponds to the 18 nm obtained with the control and LC2-reassociated myosins, suggesting that the presence of LC2 may have a role in regulating the side-to-side assembly of the myosin rods. (c) Filaments assembled from LC2-deficient myosin tend to aggregate side-by-side, but not those assembled from control and LC2-reassociated myosin. (d) The presence of MgATP has no effect on the length distribution of LC2-deficient myosin filaments in contrast to the sharpening of the distribution observed with control and reassociated myosin.     

Cellulosic nanowhiskers. Theory and application of light scattering from polydisperse spheroids in the Rayleigh-Gans-Debye regime

Mathematical treatment of light scattering within the Rayleigh-Gans-Debye limit for spheroids with polydispersity in both length and diameter is developed and experimentally tested using cellulosic nanowhiskers (CNW). Polydispersity indices are obtained by fitting the theoretical formfactor to experimental data. Good agreement is achieved using a polydispersity of 2.3 for the length, independent of the type of acid used. Diameter polydispersities are 2.1 and 3.0 for sulfuric and hydrochloric acids, respectively. These polydispersities allow the determination of average dimensions from the z-average mean-square radius (z) and the weight-average molecular weight (M w) easily obtained from Berry plots. For cotton linter hydrolyzed by hydrochloric acid, the average length and diameter are 244 and 22 nm. This compares to average length and diameter of 272 and 13 nm for sulfuric acid. This study establishes a new light-scattering methodology as a quick and robust tool for size characterization of polydisperse spheroidal nanoparticles.     

Fibrous and tubular inclusions in four xylariaceous fungi

Summary Intranuclear and cytoplasmic fibrous inclusions and cytoplasmic tubular inclusions have been studied using electron microscope techniques. The fibrous inclusions are composed of closely packed, rod-like structures. Each rod has an outside diameter of ± 24 nm, a hollow centre and lateral projections along its length. The tubular inclusions occur as densely packed bundles or loose arrays of 10–13 nm diameter tubules which are composed of subunits arranged in a double helical structure. The distribution, origin and possible function of these and similar inclusions is discussed.     

Surface Structure of Chromatium okenii and Chromatium weissei

The outermost structured layer of both Chromatium weissei and C. okenii is composed of a hexagonal array of hollow cone-shaped subunits approximately 25 nm in length and 13 nm in diameter.     

Radial density distribution of chromatin: evidence that chromatin fibers have solid centers

Fiber diameter, radial distribution of density, and radius of gyration were determined from scanning transmission electron microscopy (STEM) of unstained, frozen-dried chromatin fibers. Chromatin fibers isolated under physiological conditions (ionic strength, 124 mM) from Thyone briareus sperm (DNA linker length, n = 87 bp) and Necturus maculosus erythrocytes (n = 48 bp) were analyzed by objective image-processing techniques. The mean outer diameters were determined to be 38.0 nm (SD = 3.7 nm; SEM = 0.36 nm) and 31.2 nm (SD = 3.6 nm; SEM = 0.32 nm) for Thyone and Necturus, respectively. These data are inconsistent with the twisted-ribbon and solenoid models, which predict constant diameters of approximately 30 nm, independent of DNA linker length. Calculated radial density distributions of chromatin exhibited relatively uniform density with no central hole, although the 4-nm hole in tobacco mosaic virus (TMV) from the same micrographs was visualized clearly. The existence of density at the center of chromatin fibers is in strong disagreement with the hollow-solenoid and hollow-twisted-ribbon models, which predict central holes of 16 and 9 nm for chromatin of 38 and 31 nm diameter, respectively. The cross-sectional radii of gyration were calculated from the radial density distributions and found to be 13.6 nm for Thyone and 11.1 nm for Necturus, in good agreement with x-ray and neutron scattering. The STEM data do not support the solenoid or twisted-ribbon models for chromatin fiber structure. They do, however, support the double-helical crossed-linker models, which exhibit a strong dependence of fiber diameter upon DNA linker length and have linker DNA at the center.     

A phage in Bartonella bacilliformis.

Bacteriophage-like particles were found in Bartonella bacilliformis culture. The particles consisted of head (icosahedral), 40 nm in diameter, and tail, 16 nm in length.     

Extramembraneous particles and structural variations of tubular myelin figures in rat lung surfactant

Tubular myelin figures of pulmonary surfactant were examined by electron microscopy after fixation in glutaraldehyde and postfixation in an osmium tetroxide-ferrocyanide mixture. Bilayered membranes were seen as parallel arrays or as lattices with spacings varying from about 36 to 50 nm. This method also produced good visualization of drumstick-like particles, 5 nm in diameter and about 15 nm in length. The particles were regularly spaced at intervals of 16 nm in rows along the rectangular angles of myelin membranes. Depending on the size of the tubules the particles contacted each other in the center of the tubules at low diameters (tubular diameter less than 40 nm) and formed a continuous filamentous central core, or they were separated from one another (tubular diameter greater than 40 nm). In the latter case the central core had a hollow appearance. Based on further findings employing tannic acid, lipid extraction with 2,2-dimethoxypropane, and a ruthenium red-osmium tetroxide technique for the demonstration of polyanionic proteins it is suggested that these particles are protein in nature and that they are involved in the formation and maintenance of the structure of tubular myelin. A new concept of the ultrastructure of tubular myelin figures is proposed.     

Fibrillar and tubular fine structures in the cytoplasm of Entamoeba histolytica (author's transl)]

The electron-microscopical study of conventional fixed and contrasted Entamoeba histolytica-trophozoites from Diamonds monoxenic TTY-medium revealed "thick fibrils" in the vesicular cytoplasm of the parasites. They are 9-14 nm in diameter and are therefore considered to be myosin-like filaments, that are spread mainly in the tail or the uroid of the moving ameba. No association with microfilaments (MF) or other organelles could be observed. During the same investigation microtubules (MT) of variable length are described having a diameter of 35 nm, surrounded by a 19-25 nm wide capsule. They are distributed singly or in bundles with a maximal diameter of 350 nm. Some of the MT were coiled up to a helical shape.     

Subfilament organization in myosin filaments of the fast abdominal muscles of the lobster, Homarus americanus

The myosin filaments of the fast abdominal muscle of the lobster are about 2.7 microns long with a diameter of about 20 nm. They have a low density core in transverse sections except for a short portion in the middle of the filaments about 140 nm in length which is solid. In the solid region the diameter of the filaments is 25 nm. The wall of the filaments is made up of 12 subfilaments arranged in six pairs in a single layer around the wall. The spacing between the subfilaments of a pair is 3.4 nm and the spacing between successive pairs is 8.4 nm. An extra density is present on the inner surface of the wall of the filament along the entire length of the tubular portion of the filament. This density is always adherent to the wall and in serial transverse sections of the same filament its position changes from section to section without any apparent pattern to the change. No structural organization could be detected in this extra density.     

Nuclear inclusions in the posterior epithelium of the rat pituitary cleft]

Microfilamentous nuclear inculsions have been found at the ultrastructural level in the posterior epithelium of the rat pituitary cleft. They appear strictly located in ciliate cells of this epithelium. The microfilaments (7-8 nm in diameter) are gathered as a bundle. Their length is up to several microns and their average diameter is 0,35 micron. They can only be observed in adult rats.     

Structure of the filamentous phage pIV multimer by cryo-electron microscopy

The homo-multimeric pIV protein constitutes a channel required for the assembly and export of filamentous phage across the outer membrane of Escherichia coli. We present a 22 A-resolution three-dimensional reconstruction of detergent-solubilized pIV by cryo-electron microscopy associated with image analysis. The structure reveals a barrel-like complex, 13.5 nm in diameter and 24 nm in length, with D14 point-group symmetry, consisting of a dimer of unit multimers. Side views of each unit multimer exhibit three cylindrical domains named the N-ring, the M-ring and the C-ring. Gold labeling of pIV engineered to contain a single cysteine residue near the N or C terminus unambiguously identified the N-terminal region as the N-ring, and the C-terminal region was inferred to make up the C-ring. A large pore, ranging in inner diameter from 6.0 nm to 8.8 nm, runs through the middle of the multimer, but a central domain, the pore gate, blocks it. Moreover, the pore diameter at the N-ring is smaller than the phage particle. We therefore propose that the pIV multimer undergoes a large conformational change during phage transport, with reorganization of the central domain to open the pore, and widening at the N-ring in order to accommodate the 6.5 nm diameter phage particle.     

Self-assembly of partially hydrolysed alpha-lactalbumin

Hydrolysis of the whey protein alpha-lactalbumin with a specific serine protease has been shown to result in regular nanotubes of approximately 20 nm in outer diameter and reaching several mum in length. Tubular assembly depends on the concentration of protein as this determines how far the hydrolysis proceeds. A concentration of 30 g L(-1) is a prerequisite for tubular formation, as is a minimum concentration of calcium. At lower protein concentrations calcium-independent formation of linear fibrils (approximately 5 nm in diameter) is favoured. Possible applications of alpha-lactalbumin nanotubes include use as a viscosifier and gelling agent and also pharmaceutical utilization (such as targeted drug release) and use in nanotechnology can be envisioned.     

RecA protein self-assembly. Multiple discrete aggregation states

Light scattering, sedimentation and electron microscopy have been used to investigate the aggregation states of highly purified RecA protein in solution. We show that RecA protein will self-assemble into a discrete series of quaternary structures depending upon protein concentration, ionic environment, and nucleotide cofactors. In a stock solution at moderate concentration (10 to 50 microM) RecA protein exists as small particles approximately 4 nm in diameter, larger particles approximately 12 nm in diameter (most probably rings of RecA protein), 10 nm diameter rods varying from 50 to 200 nm in length, and finally as much larger bundles of rods. The addition of monovalent salt shifts the distribution of RecA protein between its various oligomeric states. Increasing protein concentration favors more highly aggregated structures. At a given protein concentration, addition of mM levels of MgCl2 promotes the rapid formation of rods and slow formation of bundles. Under conditions typical of in vitro strand exchange reactions, RecA protein was found to exist as a mixture of rods and 12 nm particles with relatively few monomers.     

Two Novel Bacteriophages of Thermophilic Bacteria Isolated from Deep-Sea Hydrothermal Fields

Bacteriophages of thermophiles are of great interest due to their important roles in many biogeochemical and ecological processes. However, no virion has been isolated from deep-sea thermophilic bacteria to date. In this investigation, two lytic bacteriophages (termed Bacillus virus W1 and Geobacillus virus E1) of thermophilic bacteria were purified from deep-sea hydrothermal fields in the Pacific for the first time. Bacillus virus W1 (BVW1) obtained from Bacillus sp. w13, had a long tail (300nm in length and 15 nm in width) and a hexagonal head (70 nm in diameter). Another virus, Geobacillus virus E1 (GVE1) from Geobacillus sp. E26323, was a typical Siphoviridae phage with a hexagonal head (130 nm in diameter) and a tail (180 nm in length and 30 nm in width). The two phages contained double-stranded genomic DNAs. The genomic DNA sizes of BVW1 and GVE1 were estimated to be about 18 and 41 kb, respectively. Based on SDS-PAGE of purified virions, six major proteins were revealed for each of the two phages. The findings in our study will be very helpful to realize the effect of virus on thermophiles as well as the communities in deep-sea hydrothermal fields.     

Assembly of Cellulose Synthesizing Complexes on the Plasma Membrane of Boodlea coacta

The assembly of cellulose synthesizing complexes (terminal complexes,TCs) on the plasma membrane of Boodlea coacta was investigatedduring the formation of both the matrix-rich layer (MRL) andfibril-rich layers (FRLs) of cell walls. The TCs appeared tobe located mostly within the outer leaflet of the plasma membrane,and were observed as elliptical protrusions consisting of manyparticles of about 9 nm in diameter. Their length varied from100 to 500 nm (average, 220 nm) during MRL formation and from100 to 860 nm (average, 360 nm) during FRL formation. A correlationwas found between the length of TCs and the microfibril widthin both MRL and FRL. On the E-face of the plasma membrane, numerous round protrusions(30–130 nm in diameter), consisting of many particles,8–10 nm in diameter, were also present. Their densitywas greater during FRL formation than during MRL formation.Some of these structures larger than 100 nm were associatedwith microfibril impressions and some appeared to be bound tothe TCs. These protrusions increased in number with Calcofluortreatment but decreased in number when the dye was removed fromthe culture medium. Thus, the TCs may be assembled from massesof particles aggregated on the outer surface of the plasma membrane,and may grow longer by incorporation of these masses. The appearanceof the longer TCs during FRL formation is probably due to thegreater density of these masses. (Received May 1, 1985; Accepted August 16, 1985)