Electron microscope tomography of Balbiani Ring hnRNP substructure

Three-dimensional image reconstruction of large nuclear RNP (lnRNP) particles by automated electron tomography

Nuclear RNA transcripts of split genes and their splicing products, as well as the general population of nuclear polyadenylated RNA are packaged in multi-component large nuclear ribonucleoprotein (lnRNP) particles. These lnRNP particles, which sediment at the 200 S region in sucrose gradients, contain all U small nuclear RNPs required for precursor messenger RNA (pre-mRNA) splicing and several protein splicing factors, including U2AF and the SR proteins. Electron microscopy of lnRNP particles revealed a large compact structure of 50 nm in diameter. In this study we employed automated computed tomography from electron micrographs for the three-dimensional (3D) image reconstruction of individual lnRNP particles isolated from mammalian cells nuclei and negatively stained. For each particle, a tilt series of 71 images was collected by direct digital recording of the images on a CCD camera attached to a computer controlled TEM facility. The 3D image was reconstructed according to the back projection principle. For rendering, real time display and comparison of the reconstructed particles, interactive computer graphics was employed. The reconstructed 3D images show a compact structure composed of four major subunits connected to each other. Comparison of the reconstructed lnRNP particles revealed morphological similarity of the individual particles, as well as similarity among the sub-structures. Based on these observations we propose a model for the packaging of nuclear pre-mRNAs in lnRNP particles where each substructure represents a functional unit. This model is compatible with the requirements for alternative splicing in multi-intronic pre-mRNAs, and with the fact that the splicing of multi-intronic pre-mRNAs does not occur in a sequential manner.

Electron spectroscopic imaging analyses of the distribution of phosphorus in Balbiani ring granules and in the surrounding nucleoplasm

The in situ distribution of phosphorus was studied in unstained ultrathin sections of salivary glands of Chironomus tentans and Ch. thummi larvae using elemental mapping by means of an energy-filtering transmission electron microscope. This distribution was related to the structures observed using contrast enhancement with inelastically scattered electrons at 250 eV. This procedure demonstrated that a phosphorus-containing fibril about 2 nm thick is the common substructure of the following nuclear ribonucleoprotein structural constituents: the Balbiani ring granules, their precursor fibrils seen at the sites of transcription, especially at the Balbiani rings, and the fibres traversing the pore of the nuclear envelope. These phosphorus-containing thin fibrils are sensitive to RNase. Thicker substructural features of the Balbiani ring granules, occurring as a curved ribbon on a dense particle, appear to be formed by the dense packing of the fine fibrils. The Balbiani ring granules located near the nuclear envelope are often linked to it by fine filaments.

Alignment of electron tomographic series by correlation without the use of gold particles

Electron tomography requires that a tilt series of micrographs be aligned and that the orientation of the tilt axis be known. This has been done conveniently with gold markers applied to the surface of a specimen to provide easily accessible information on the orientation of each tilt projection. Where gold markers are absent, another approach to alignment must be used. A method is presented here for aligning tilt projections without the use of markers, utilizing correlation methods. The technique is iterative, drawing principally on the work of Dengler [Ultramicroscopy 30 (1989) 337], and consists of computing a low resolution back projection image from which computed tomographic projections can be generated. These in turn serve as reference images for the next alignment of the tomographic series. An initial alignment must be made before the first back projection, and this is done following the method of Guckenberger [Ultramicroscopy 9 (1982) 167] for translational alignment and by common lines analysis [Liu et al., Ultramicroscopy 58 (1995) 393] for identification of the tilt axis. Four tomographic series of a biological nature were aligned and analyzed, and the method has proven to be both accurate and reproducible for the data presented here.

Double-tilt electron tomography

Fidelity of tomographic reconstructions is improved and reconstruction artifacts are reduced, without increasing the number of projections, by combining tilt series taken around two orthogonal axes. Test reconstructions were made from high-voltage EM of rat liver mitochondria in a 0.6 micron thick plastic section. A number of schemes for selecting tilt angles for the projections are compared. A new method for aligning fiducial markers is described. It uses an iterative algorithm to determine the shift, scale, in-plane rotation and tilt angle for each tilt image, enforcing agreement of the expected locations of the fiducial markers in 3D space. These 3D locations are used to find the orientation between two tilt series and to merge both sets of projections.

EM-tomography of section collapse, a non-linear phenomenon

Using back projection for reconstruction and tilt series of Epon or Lowicryl embedded and sectioned material, we demonstrated: (1) a reduction in thickness of 50% for Epon and 80% for Lowicryl sections, and (2) a non-uniform density distribution along the electron-optical axis in sections. The highest density was found at the vacuum exposed side of the section. The formvar side of the section showed a similar increase in density, but not to the same extent. Minimalization of electron exposure, even without pre-exposure, did not affect the reconstructed thickness, nor did it affect the non-uniform density distribution. However, parallax measurements showed that at 150K, collapse of Epon sections does not take place. For EM-tomography of plastic embedded material our findings imply that at the top and bottom portion of the sections the dimensions of the reconstructed structures are distorted, but that in the middle portion the dimensions are reliably retained.

Approaches to large-scale structures

Quantitative three-dimensional (3D) maps of large-scale structures can now be routinely obtained by the use of high- or intermediate-voltage electron tomography. The recent 3D reconstructions of the mitochondrion and the Golgi apparatus highlight both the potential and the shortcomings of this technique. New technological developments, in particular the development of automated low-dose electron tomography, are expected to facilitate the 3D visualization of large structures in the fully hydrated environment, embedded in vitreous ice.

Modeling the 3-D RNA distribution in the Balbiani ring granule

Mature Balbiani Ring (BR) granules in situ were stained with the nucleic acid specific stain, osmium ammine-B, recorded by electron spectroscopic imaging and reconstructed by electron microscope tomography to examine the three-dimensional (3-D) distribution of BR heterogeneous nuclear RNA (hnRNA). The BR2 granules contain ca. 37 kb of mRNA. Reconstructed BR granules were selected to emphasize one of the prevalent conformations seen in the sectioned salivary glands, the en face or "pin-wheel" conformation. A variety of image processing and volume-rendering operations were applied to the set of reconstructed BR granules. Some of the conclusions of this study are the following: (1) RNA distribution is not uniform throughout the granule; (2) RNA is condensed into about ten particles per granule, which all appear to possess approximately the same RNA stain density; (3) heterogeneity exists in the positions and sizes of particles within the various BR granules. These data argue for the folding of a beaded ribbon, consisting of connected particulate condensations of BR mRNA, possessing considerable 3-D flexibility, even in the packaged state. A comparison of this beaded-ribbon model and a prior folded hnRNP fiber model is also presented.

The Balbiani ring particle: a model for the assembly and export of RNPs from the nucleus?

Balbiani rings are exceptionally large puffs on the polytene chromosomes in the dipteran Chironomus tentans. These puffs are particularly well suited for studies of the structure of active genes and the synthesis and transport of specific RNA-protein (RNP) particles. The Balbiani ring RNP particle consists of a ribbon bent into a ring-like structure, the ribbon being built from a tightly folded 7 nm RNP filament. The assembly of the particle takes place concomitant with transcription and occurs in a stepwise fashion. As the particle is transported through the nuclear pore the ribbon straightens out, with the 5' end of the transcript leading. During translocation the tightly packed RNP filament is gradually unfolded, and on the cytoplasmic side the mRNA is immediately engaged in polysome formation.