Advances in image processing for electron microscopy: Part I

Some trends in microscope image processing

The present review tries to identify some trends among the multitude of ways followed by image processing developments in the field of microscopy. Nine topics were selected. They cover the fields of: signal processing, statistical analysis, artificial intelligence, three-dimensional microscopy, multidimensional microscopy, multimodality microscopy, theory, simulation and multidisciplinarity. A specific topic is dedicated to a trend towards semi-automation instead of full automation in image processing.

3-d reconstruction of 2-D crystals in real space

A new algorithm for three-dimensional reconstruction of two-dimensional crystals from projections is presented, and its applicability to biological macromolecules imaged using transmission electron microscopy (TEM) is investigated. Its main departures from the traditional approach is that it works in real space, rather than in Fourier space, and it is iterative. This has the advantage of making it convenient to introduce additional constraints (such as the support of the function to be reconstructed, which may be known from alternative measurements) and has the potential of more accurately modeling the TEM image formation process. Phantom experiments indicate the superiority of the new approach even without the introduction of constraints in addition to the projection data.

Reversible binding of glycolytic enzymes and size change in the actin-containing filaments of the frog skeletal muscle

Electron microscopy was used in order to study the change of the actin-containing filaments when the bound glycolytic enzymes were removed by a high ionic strength solution. The effectiveness of the extraction medium was checked by estimating the aldolase activity released. Evidence was provided that the larger diameter of the actin filaments in the I-bands in comparison with the A-bands can be accounted for by the bound glycolytic enzymes.

Molecular organization of Mason-Pfizer monkey virus capsids assembled from Gag polyprotein in Escherichia coli

We describe the results of a study by electron microscopy and image processing of Gag protein shells-immature capsids--of Mason-Pfizer monkey virus assembled in Escherichia coli from two truncated forms of the Gag precursor: Deltap4Gag, in which the C-terminal p4Gag was deleted, and Pro(-)CA.NC, in which the N-terminal peptides and proline 1 of the CA domain were deleted. Negative staining of capsids revealed small patches of holes forming a trigonal or hexagonal pattern most clearly visible on occasional tubular forms. The center-to-center spacing of holes in the network was 7.1 nm in Deltap4Gag capsids and 7.4 nm in Pro(-)CA.NC capsids. Image processing of Deltap4Gag tubes revealed a hexagonal network of holes formed by six subunits with a single subunit shared between rings. This organization suggests that the six subunits are contributed by three trimers of the truncated Gag precursor. Similar molecular organization was observed in negatively stained Pro(-)CA.NC capsids. Shadowed replicas of freeze-etched capsids produced by either construct confirmed the presence of a hexagonal network of holes with a similar center-to-center spacing. We conclude that the basic building block of the cage-like network is a trimer of the Deltap4Gag or Pro(-)CA.NC domains. In addition, our results point to a key role of structurally constrained CA domain in the trimeric interaction of the Gag polyprotein.

Ribosomal dynamics explored by cryo-electron microscopy

Cryo-electron microscopy has furnished direct evidence for conformational changes of the ribosome as it proceeds, in a cyclic manner, through different functional states. Strategies to explore the ribosome dynamics include trapping of particular functionally meaningful states by chemical, genetic, or physical means. The new atomic information obtained by X-ray crystallography should make it possible to track conformational changes observed by cryo-electron microscopy to changes of the underlying structural framework of the ribosome.

Electron microscopy and x-ray diffraction studies of Lotus tetragonolobus A isolectin cross-linked with a divalent Lewisx oligosaccharide, an oncofetal antigen

The interactions of lectins with multivalent carbohydrates often leads to the formation of highly ordered cross-linked lattices that are amenable to structural studies. A particularly well ordered, two-dimensional lattice is formed from fucose-specific isolectin A from Lotus tetragonolobus cross-linked with difucosyllacto-N-neohexaose, an oligosaccharide possessing the Lewisx determinant, which is an oncofetal antigen. A combination of electron microscopy, x-ray diffraction, simulation of electron micrographs, and molecular model building was used to determine the relative positions of the tetrameric lectin and bivalent carbohydrate within the lattice. X-ray diffraction from unoriented pellets was used to determine the lattice dimensions and analysis of electron micrographs was used to determine the lattice symmetry. Molecular models of the lattice were constructed based on the known structure of the jack bean lectin concanavalin A and the high degree of sequence homology between the two lectins. Using the symmetry and dimensions of the lattice and its appearance in filtered electron micrographs, molecular models were used to determine the orientation of the lectin in the lattice, and to define the range of lectin-oligosaccharide interactions consistent with the structural data. The present study provides the first description of a highly ordered, two-dimensional, cross-linked lattice between a tetravalent lectin and a bivalent carbohydrate.

Fourier analysis of electron micrographs of positively stained collagen fibrils: application to type I and II collagen typing

Type I and II collagen (native-type) fibrils, positively stained with uranyl acetate, present typical periodic (D = 67 nm) cross-striation patterns. Although the two patterns are similar, the distributions of charged amino acids along the type I and II collagen molecules are different. After optical diffraction analysis or computer image processing of electron micrographs, different Fourier transforms were obtained from type I and II collagen fibrils, either as native fibrils or after in vitro reconstitution from purified molecules. With tissues such as tendon and cartilage, better results were obtained after mild trypsin treatment, which allowed better isolation and staining of the collagen fibrils. The main difference observed in the Fourier transforms was the presence in type II collagen fibrils of a strong tenth-order peak (corresponding to the tenth harmonic of the fundamental frequency). In order to discriminate between the two collagens, we measured the ratio (R) of the areas under the ninth- and tenth-order peaks. In trypsin treated tissues, the distributions of these ratios were clearly separated: below 1.0 for type II collagen fibrils and above 1.5 for type I collagen fibrils. This method appears to be suitable for rapid typing of type I and II collagen fibrils and might be useful for determining the exact composition of fibrils in tissues, such as intervertebral discs, that contain these both types of collagen.

Structural study of the response regulator HupR from Rhodobacter capsulatus. Electron microscopy of two-dimensional crystals on a nickel-chelating lipid

Two-dimensional crystals of the histidine-tagged-HupR protein, a transcriptional regulator from the photosynthetic bacterium Rhodobacter capsulatus, were obtained upon specific interaction with a Ni2+-chelated lipid monolayer. HupR is a response regulator of the NtrC family; it activates the transcription of the structural genes, hupSLC, of the [NiFe]hydrogenase. The lipid (Ni-NTA-DOGA) uses the metal chelator nitrilotriacetic group as the hydrophilic headgroup and contains unsaturated oleyl tails to provide the fluidity necessary for two-dimensional protein crystallization. A projection map of the full-length protein at 18 A resolution was generated by analysing electron microscopy micrographs of negatively stained crystals. The HupR protein appeared to be dimeric and revealed a characteristic "propeller-like" motif. Each monomer forms an L-shaped structure.

Changes in macromolecular organization in collagen assemblies during secretion in the nidamental gland and formation of the egg capsule wall in the dogfish Scyliorhinus canicula

The thickest layer (L 2 ) of the egg capsule wall of the dogfish, Scyliorhinus Canicula , is constructed largely from highly ordered collagen fibrils (Knight & Hunt 1976). This collagen is stored and secreted by the nidamental gland and passes through an extraordinary series of ordered phases, m any of which have well defined liquid crystalline structure. We have examined the changes in macromolecular packing of the collagen as it moves from the cisternae of the endoplasmic reticulum to secretory granules, is secreted and then formed into the egg capsule wall. Within the endoplasmic reticulum cisternae the collagen appears anisotropic but becomes assembled into a smectic A or lamellar phase in the Golgi cisternae. This phase persists in early secretory granules, where it is found in conjunction with a micellar phase. As these granules mature, the collagen passes through a cholesteric mesophase before adopting a columnar hexagonal arrangement. On merocrine secretion the granules’ contents revert rapidly to the smectic A-lamellar and micellar phases. As it passes along the nidamental gland tubules, the collagen is first converted into a second distinct micellar phase before assembling into the final fibrils that constitute the egg capsule. These phase transitions give powerful insights into the way in which the macromolecular arrangement of collagen molecules can be modulated and are discussed in the context of a range of other related structural transitions in collagens.

Electron microscopic image analysis of cardiac gap junction membrane crystals

Cardiac gap junctions play an important functional role in the myocardium by electrically coupling adjacent cells, thereby providing a low resistance pathway for cell-to-cell propagation of the action potential. Two-dimensional crystallization of biochemically isolated rat ventricular gap junctions has been accomplished by an in situ method in which membrane suspensions are sequentially dialyzed against low concentrations of deoxycholate and dodecyl-beta-D-maltoside. Lipids are partially extracted without solubilizing the protein, and the increased protein concentration facilitates two-dimensional crystallization in the native membrane environment. The two-dimensional crystals have a nominal resolution of 16 A and display plane group symmetry p6 with a = b = 85 A and gamma = 120 degrees. Projection density maps show that the connexons in cardiac gap junctions are formed by a hexameric cluster of alpha 1 connexin subunits. Protease cleavage of alpha 1 connexin from 43 to 30 kDa releases approximately 13kDa from the carboxy-tail, and the projection density maps are not significantly altered. Uranyl acetate stain penetrates the ion channel, whereas phosphotungstic acid is preferentially deposited over the lipid regions. This differential staining can be used to selectively probe the central channel of the connexon and the interface between the connexon and the lipid. The hexameric design of alpha 1 connexons appears to be a recurring quaternary motif for the multigene family of gap junction proteins.

Teaching electron diffraction and imaging of macromolecules

Electron microscopic analysis can be used to determine the three-dimensional structures of macromolecules at resolutions ranging between 3 and 30 A. It differs from nuclear magnetic resonance spectroscopy or x-ray crystallography in that it allows an object's Coulomb potential functions to be determined directly from images and can be used to study relatively complex macromolecular assemblies in a crystalline or noncrystalline state. Electron imaging already has provided valuable structural information about various biological systems, including membrane proteins, protein-nucleic acid complexes, contractile and motile protein assemblies, viruses, and transport complexes for ions or macromolecules. This article, organized as a series of lectures, presents the biophysical principles of three-dimensional analysis of objects possessing different symmetries.

Surface layers of bacteria

Since bacteria are so small, microscopy has traditionally been used to study them as individual cells. To this end, electron microscopy has been a most powerful tool for studying bacterial surfaces; the viewing of macromolecular arrangements of some surfaces is now possible. This review compares older conventional electron-microscopic methods with new cryotechniques currently available and the results each has produced. Emphasis is not placed on the methodology but, rather, on the importance of the results in terms of our perception of the makeup and function of bacterial surfaces and their interaction with the surrounding environment.

Role of the S layer in morphogenesis and cell division of the archaebacterium Methanocorpusculum sinense

Thin sections, freeze-etched, and negatively stained preparations of Methanocorpusculum sinense cells reveal a highly lobed cell structure with a hexagonally arranged surface layer (S layer). Digital image processing of negatively stained envelope fragments show that the S layer forms a porous but strongly interconnected network. Since the S layer is the exclusive cell envelope component outside the cytoplasmic membrane it must have a cell shape determining and maintaining function. Although lattice faults such as disclinations and dislocations are a geometrical necessity on the surface of a closed protein crystal, our data indicate that they also play important roles as sites for the incorporation of new morphological units, in the formation of the lobed cell structure, and in the cell division process. In freeze-etched preparations of intact cells numerous positive and negative 60 degree wedge disclinations can be detected which form pentagons and heptagons in the hexagonal array. Complementary pairs of pentagons and heptagons are the termination points of edge dislocations. They can be expected to function both as sites for incorporation of new morphological units into the lattice and as initiation points for the cell division process. The latter is determined by the ratio between the increase of protoplast volume and the increase in actual S-layer surface area during cell growth. We postulate that this mode of cell fission represents a common feature in lobed archaebacteria which possess an S layer as the exclusive wall component.

Macromolecular structure and aggregation states of Helicobacter pylori urease

Urease purified from Helicobacter pylori by differential ultracentrifugation and fast pressure liquid chromatography was composed of subunits with apparent molecular weights (MrS) of 66,000 and 30,000. Electron microscopy of this purified material demonstrated that it formed disc-shaped macromolecular aggregates that were approximately 13 nm in diameter and 3 nm thick. Images of both negatively stained and shadowed preparations indicated that the discs tended to stack to form pairs and then these pairs further aggregated to form four-disc stacks. This stacking of subunits explains the heterogeneity observed previously in the molecular weight of urease preparations. In some negatively stained preparations there were also some smaller (approximately 8-nm-diameter) annular units present, which may represent individual urease units or possibly an aggregate of one of the two subunits from which urease is constructed.

Similar features in Z bands of both skeletal and cardiac muscle revealed by image enhancement

We have shown previously that the small square (ss) and basket weave (bw) states of the Z band lattice in cardiac and skeletal muscle are related to the contractile state of the muscle. We have used two-dimensional image processing techniques on digitized electron micrographs to enhance the structural features of each projected lattice form in cardiac and skeletal muscle. Four different processing techniques were employed to assess the effect of enhancement artifacts on the resulting Z band images. We observed only slight differences between enhanced images of a particular Z band form produced by the four different techniques. Every enhanced image showed an approximate four-fold symmetry independent of muscle type or Z band lattice form. Each enhanced image showed four cross-connecting Z-filaments which appeared to connect each axial filament to the four nearest axial filaments. In bw images from both cardiac and skeletal muscle, axial filaments had a greater apparent diameter and a greater interaxial filament spacing than in the ss images. In both muscle types, the cross-connecting Z-filaments appeared to overlap half-way between axial filaments in the ss images while the bw images showed no such overlap. These structural features are consistent with a dynamic Z band lattice that participates in muscle contraction.

Human endothelial actin-binding protein (ABP-280, nonmuscle filamin): a molecular leaf spring

Actin-binding protein (ABP-280, nonmuscle filamin) is a ubiquitous dimeric actin cross-linking phosphoprotein of peripheral cytoplasm, where it promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. The complete nucleotide sequence of human endothelial cell ABP cDNA predicts a polypeptide subunit chain of 2,647 amino acids, corresponding to 280 kD, also the mass derived from physical measurements of the native protein. The actin-binding domain is near the amino-terminus of the subunit where the amino acid sequence is similar to other actin filament binding proteins, including alpha-actinin, beta-spectrin, dystrophin, and Dictyostelium abp-120. The remaining 90% of the sequence comprises 24 repeats, each approximately 96 residues long, predicted to have stretches of beta-sheet secondary structure interspersed with turns. The first 15 repeats may have substantial intrachain hydrophobic interactions and overlap in a staggered fashion to yield a backbone with mechanical resilience. Sequence insertions immediately before repeats 16 and 24 predict two hinges in the molecule near points where rotary-shadowed molecules appear to swivel in electron micrographs. Both putative hinge regions are susceptible to cleavage by proteases and the second also contains the site that binds the platelet glycoprotein Ib/IX complex. Phosphorylation consensus sequences are also located in the hinges or near them. Degeneracy within every even-numbered repeat between 16 and 24 and the insertion before repeat 24 may convert interactions within chains to interactions between chains to account for dimer formation within a domain of 7 kD at the carboxy-terminus. The structure of ABP dimers resembles a leaf spring. Interchain interactions hold the leaves firmly together at one end, whereas intrachain hydrophobic bonds reinforce the arms of the spring where the leaves diverge, making it sufficiently stiff to promote high-angle branching of actin filaments. The large size of the leaves, their interruption by two hinges and flexible actin-binding site, facilitate cross-linking of widely dispersed actin filaments.

Structural and chemical characterization of the S layer of a Pseudomonas-like bacterium

Sections and freeze-fractured preparations showed an S layer on the surface of Pseudomonas-like strain EU2. Polyacrylamide gel electrophoresis of cell envelopes extracted with 1% sodium dodecyl sulfate (SDS) at room temperature showed three proteins (45K, 55K, and 110K). The 55K protein was identified as the S-layer protein. Incubation in 1.5 M guanidine hydrochloride removed the S layer from cell envelopes and dissociated the structure into subunits. The soluble 55K protein reassembled into planar sheets upon removal of the guanidine hydrochloride by dialysis. Electron microscopy and image processing indicated that these sheets had p4 symmetry in projection with a lattice constant of 13.2 +/- 0.1 nm (corresponding to 9.3 nm between adjacent fourfold axes). In some instances these reassemblies appeared to form small three-dimensional crystals which gave particularly clear views of the structure in projection because of the superimposition of information from a number of layers. A model is proposed with molecules having rounded lobes connected by a narrower linker region and joining at the lobes to form the fourfold axes of the array. The pattern superficially resembles those of other bacterial S layers, such as those of Aeromonas salmonicida, Aeromonas hydrophila, and Azotobacter vinelandii. Extraction of cell envelopes with 1% SDS at 50 degrees C released the 110K protein from the envelopes and removed an amorphous backing layer from the S layer. The 45K protein displayed heat-modifiable migration in SDS-polyacrylamide gel electrophoresis and was insoluble in SDS at 50 degrees C or in high concentrations of guanidine hydrochloride, suggesting that it was associated with the peptidoglycan.

Two structural states of the vertebrate Z band

Ultrastructural analysis of the vertebrate Z band suggests that two reversible states of a single intricate lattice are essential for the contractile process. The two structural states of the Z band lattice (ss and bw) have been described in cross section in skeletal and cardiac muscle in different physiological states. The lattice responds to active tension but resists passive deformation. Changes in Z band form and dimension are correlated with cross-bridge binding. Two-dimensional image processing techniques show enhanced structural features that vary with the observed changes in lattice dimension. All projected images from all lattices show an approximate four-fold symmetry. Each image reveals differences in the appearance of axial filaments which enter from opposite sides of the Z band and cross-connecting filaments of similar curvature which appear to connect each axial filament to four nearest axial filaments. In the ss images, the apparent diameter of cross-cut axial filaments and the Z band interaxial filament spacing are smaller than in bw images. Cross-connecting filaments appear to overlap in the region half-way between axial filaments in ss images. We conclude that the Z band is an essential and dynamic part of the sarcomere, uniquely suited to transmit tension while maintaining dimensions appropriate for cross-bridge interaction.

The Dictyostelium gelation factor shares a putative actin binding site with alpha-actinins and dystrophin and also has a rod domain containing six 100-residue motifs that appear to have a cross-beta conformation

The 120-kD gelation factor and alpha-actinin are among the most abundant F-actin cross-linking proteins in Dictyostelium discoideum. Both molecules are homodimers and have extended rod-like configurations that are respectively approximately 35 and 40 nm long. Here we report the complete cDNA sequence of the 120-kD gelation factor which codes for a protein of 857 amino acids. Its calculated molecular mass is 92.2 kD which is considerably smaller than suggested by its mobility in SDS-PAGE. Analysis of the sequence shows a region that is highly homologous to D. discoideum alpha-actinin, chicken fibroblast alpha-actinin, and human dystrophin. This conserved domain probably represents an actin binding site that is connected to the rod-forming part of the molecule via a highly charged stretch of amino acids. Whereas the sequence of alpha-actinin (Noegel, A., W. Witke, and M. Schleicher. 1987. FEBS [Fed. Eur. Biochem. Soc.] Lett. 221:391-396) suggests that the extended rod domain of the molecule is based on four spectrin-like repeats with high alpha-helix potential, the rod domain of the 120-kD gelation factor is constructed from six 100-residue repeats that have a high content of glycine and proline residues and which, in contrast to alpha-actinin, do not appear to have a high alpha-helical content. These repeats show a distinctive pattern of regions that have high beta-sheet potential alternating with short zones rich in residues with a high potential for turns. This observation suggests that each 100-residue motif has a cross-beta conformation with approximately nine sheets arranged perpendicular to the long axis of the molecule. In the high beta-potential zones every second residue is often hydrophobic. In a cross-beta structure, this pattern would result in one side of the domain having a surface rich in hydrophobic side chains which could account for the dimerization of the 120-kD gelation factor subunits.

Digital image processing of crystalline specimens examined by electron microscopy

Crystalline specimens imaged in the electron microscope are analysed using digital processing. Some principles of structural analysis using the method of Fourier decomposition are discussed. Complementary techniques, such as enhancement by gradient and Laplacian operators, have been found useful in analysing electron micrographs. The application of these techniques to some problems in Materials Science and Biology are reviewed. By selecting and phase-correcting spots in the computed diffraction pattern, it was possible to localize atoms, molecules, and their defective arrangement in evaporated gold, sputter-deposited tungsten films, and single crystals of cadmium selenide. Digital processing based on the theory of helical diffraction was used to explore the three-dimensional arrangement of molecules in cellular components of alveolar soft part sarcoma, Hirano bodies, and neurofibrillar tangles in the human brain.

Computer image processing of electron micrographs of biological structures with helical symmetry

Methods are described for the analysis of electron micrographs of biological objects with helical symmetry and for the production of three-dimensional models of these structures using computer image reconstruction methods. Fourier-based processing of one- and two-dimensionally ordered planar arrays is described by way of introduction, before analysing the special properties of helices and their transforms. Conceiving helical objects as a sum of helical waves (analogous to the sum of planar waves used to describe a planar crystal) is shown to facilitate analysis and enable three-dimensional models to be produced, often from a single view of the object. The corresponding Fourier transform of such a sum of helical waves consists of a sum of Bessel function terms along layer lines. Special problems deriving from the overlapping along layer lines of terms of different Bessel order are discussed, and methods to separate these terms, based on analysing a number of different azimuthal views of the object by least squares, are described. Corrections to alleviate many technical and specimen-related problems are discussed in conjunction with a consideration of the computer methods used to actually process an image. A range of examples of helical objects, including viruses, microtubules, flagella, actin, and myosin filaments, are discussed to illustrate the range of problems that can be addressed by computer reconstruction methods.