Tracing the path of messenger RNA on the Escherichia coli small ribosomal subunit. Immune electron microscopy using defined oligodeoxynucleotide analogs of mRNA

The ribosome-structure and functional ligand-binding experiments using cryo-electron microscopy

Cryo-electron microscopy has greatly advanced our understanding of the basic steps of protein synthesis in the bacterial ribosome. This article gives an overview of what has been achieved so far. Through three-dimensional visualization of complexes that represent the ribosome in defined binding states, locations were derived for the tRNA in A, P, and E sites, as well as the elongation factors. In addition, the pathways of messenger RNA and the exiting polypeptide chain could be inferred.

The three-dimensional structure of the ribosome and its components

Exciting progress has been made in the last decade by those who use physical methods to study the structure of the ribosome and its components. The structures of 10 ribosomal proteins and three isolated ribosomal protein domains are known, and the conformations of a significant number of rRNA sequences have been determined. Electron microscopists have made major advances in the analysis of images of ribosomes, and microscopically derived ribosome models at resolutions approaching 10A are likely quite soon. Furthermore, ribosome crystallographers are on the verge of phasing the diffraction patterns they have had for several years, and near-atomic resolution models for entire ribosomal subunits could emerge from this source at any time. The literature relevant to these developments is reviewed below.

Small angle scattering in ribosomal structure research: localization of the messenger RNA within ribosomal elongation states

Besides EM and biochemical studies small angle scattering (SAS) examinations have contributed significantly to our current knowledge about the ribosomal structure. SAS does not only allow the validation of competing models but permits independent model building. However, the major contribution of SAS to ribosomal structure research derived from its ability to reveal the spatial distribution of the individual ribosomal components (57 in the E. coli ribosome) within the ribosomal structure. More recently, an improved scattering method (proton-spin contrast variation) made it possible also to address the question of mapping functional ligands in defined ribosomal elongation states. Here, we review the contributions of SAS to the current understanding of the ribosome. Furthermore we present the direct localization of a small mRNA fragment within 70S elongation complexes and describe its movement upon the translocation reaction. The successful mapping of this fragment comprising only about 0.6% of the total mass of the complex proves that proton-spin contrast-variation is a powerful tool in modern ribosome research.

Cleavage of 16S rRNA within the ribosome by mRNA modified in the A-site codon with phenanthroline-Cu(II)

Cleavage of 16S rRNA was obtained through mRNA modified at position +5 with the chemical cleavage agent 1,10-o-phenanthroline. In the presence of Cu2+, and after addition of reducing agent to the modified mRNA-70S complex, cleavage of proximal nucleotides within the 16S rRNA occurred. Primer extension analysis of 16S rRNA fragments revealed that nucleotides 528-532, 1196, and 1396-1397 were cleaved. Nucleotides 1053-1055 were also cleaved but did not show the same level of specificity as the former. These results provide evidence that at some point in the translation process these regions are all within 15 A of position +5, the A-site codon, on the mRNA.

A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome

The morphology of the Escherichia coli ribosome, i.e., its shape at moderate to low (20-40 A (1 A = 0.1 nm)) resolution, provides important constraints in modeling both the folding of ribosomal RNA and the translational process. A new reconstruction, obtained by low-dose cryoelectron microscopy and image processing of single ribosomes, contains clues to the way in which the ribosome interacts with the key functional ligands: the mRNA and the A- and P-site tRNAs. It also suggests possible pathways of the nascent polypeptide chain. From an interpretation of these clues in the light of existing knowledge, a plausible model for the locations and interactions of key components of protein synthesis is suggested.

A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome

The ribosome is formed by assembly of proteins and nucleic acids, and synthesizes proteins according to genetic instructions in all organisms. Many of the biochemical steps of this fundamental process are known, but a detailed understanding requires a well-defined structural model of the ribosome. Electron microscopy combined with image reconstruction of two-dimensional crystals or single ribosomes has been the most promising technique, but the resolution of the resulting models has been insufficient. Here we report a 25-A reconstruction of the ribosome from Escherichia coli, obtained by combining 4,300 projections of ice-embedded single particles. Our new reconstruction reveals a channel in the small ribosomal subunit and a bifurcating tunnel in the large subunit which may constitute pathways for the incoming message and the nascent polypeptide chain, respectively. Based on these new findings, a three-dimensional model of the basic framework of protein synthesis is presented.

Purification of the spliceosome A-complex and its visualization by electron microscopy

Pre-mRNA splicing occurs on spliceosomes, a family of ribonucleoprotein particles. Spliceosome assembly on exogenous adenovirus pre-mRNA was blocked at the A-complex (or pre-spliceosome) stage, either by destruction of the small nuclear ribonucleoproteins (snRNPs) that comprise the U4/U5/U6 tri-snRNP complex, or by interference in tri-snRNP assembly and interactions. The A-complex was isolated by size exclusion chromatography; homogeneity was shown by electrophoresis in nondenaturing polyacrylamide gels, gradient sedimentation, and electron microscopy. Northern hybridization showed U1 and U2 snRNAs to be present in the preparation, but not U4, U5, or U6. Antibodies specific for a component of the U1 snRNP or for a component that is common to all snRNPs (except U6) each precipitated an A-complex containing pre-mRNA, U1 and U2 snRNPs. Electron micrographs showed 230 x 270-A particles whose two components appear similar to individual U1 and U2 snRNPs. Electron micrographs of an A-complex-5'-biotinyl oligonucleotide-streptavidin-gold composite allowed identification of the U2 snRNP within the structure and the localization of the 5'-segment of U2 snRNA at a unique site in the A-complex. This region of U2 RNA is adjacent to the developing catalytic center of the spliceosome.

Prokaryotic translation: the interactive pathway leading to initiation

Finding answers to the many open questions concerning the mechanism and control of prokaryotic translation remains one of the central challenges of molecular biology. In fact, recent experimental data even force us to reconsider aspects that were previously thought to be established fact. Here, we attempt a synthesis of new and not-so-new information, which leads to a revised and testable working hypothesis for translational initiation.