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

Cryoelectron microscopy and cryoelectron tomography of the nuclear pre-mRNA processing machine

Large nuclear ribonucleoprotein particles, which can be viewed as the naturally assembled precursor messenger RNA (pre-mRNA) processing machine, were analyzed in frozen-hydrated preparations by cryoelectron microscopy. A general and reproducible strategy for preparing ice-embedded large nuclear ribonucleoprotein (lnRNP) particles at sufficiently high concentration was developed. Taking advantage of their negatively charged components, the lnRNP particles are adsorbed and thus concentrated on a positively charged lipid monolayer while preserving their native structure. Using this approach we carried out cryoelectron tomography and three-dimensional image reconstruction of individual lnRNP particles. The study revealed a structure similar to that of negatively stained particles studied previously, yet with additional features. The small additional domain visualized in negative stain appeared to be larger in the ice preparations. In addition, using image restoration from focus series of ice-embedded lnRNP particles, new features such as holes within the subunits were visualized in two dimensions, and it was shown that the subunits are interconnected via a fiber, very likely formed by the pre-mRNA. This finding supports the model that each subunit represents a spliceosome that splices out the intron wound around it.

Automated electron tomography of large nuclear RNP (InRNP) particles--the naturally assembled complexes of precursor messenger RNA and splicing factors

Splicing of nuclear pre-mRNA is an important step in the regulation of gene expression as only correctly spliced mRNAs will be exported to the cytoplasm to function in protein synthesis. Nuclear RNA transcripts of split genes and their splicing products, as well as the general population of nuclear polyadenylated RNA, are packaged in multicomponent large nuclear ribonucleoprotein (lnRNP) particles. These lnRNP particles, which sediment at the 200S region in sucrose gradients, contain all U snRNPs required for pre-mRNA splicing and several protein splicing factors, including U2AF and the SR proteins and can thus be viewed as naturally assembled complexes of pre-mRNA and splicing factors. We have previously reconstructed the three-dimensional image of negatively stained individual lnRNP particles by automated electron tomography. The reconstruction revealed a compact structure, 50 nm in diameter, composed of four major subunits. Here we further analyzed the reconstructed models and the apparent connectivity between the subunits using a new rendering technique. The uniformity of the lnRNP particles was substantiated by measurement of the volume engulfed by their surface. This study further supports the model proposed 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 multiintronic pre-mRNAs, and with the fact that the splicing of multiintronic pre-mRNAs does not occur in a sequential manner.

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.

Three-point repositioning of axes: three-dimensional alignment procedure for electron microscope tomography using three markers

A description is given of a new procedure to align series of tilted graphs, made with an electron microscope, for computer tomographic purposes. The procedure uses the coordinates of three projected markers to calculate parameters needed for the reconstruction. To that end the procedure computes the direction of the tilt-axis, the translation and rotation parameters, the tilt-angle of every micrograph, and the spatial coordinates of the individual markers with their centre of gravity as origin of the coordinate system. A searching technique, based on cross-correlation, is described to locate accurately the micrographs markers.

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.