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M Boublik

Publications and source records attributed to M Boublik.

At least 37 records · Page 2Linked to original sources
PubMed1987

In vitro synthesis of 16S ribosomal RNA containing single base changes and assembly into a functional 30S ribosome.

Functional 30S ribosomes were reconstructed from total Escherichia coli 30S ribosomal proteins and 16S ribosomal RNA synthesized in vitro by T7 RNA polymerase. Up to 700 mol of RNA/mol of template could be obtained. The transcript lacked all ten normally modified bases and had three additional 5' G residues, an A----G change at position 2, and, in 22% of the molecules, one or two extra 3' residues. The synthetic 16S RNA could be assembled into a particle that cosedimented with authentic 30S and was indistinguishable from 30S by electron microscopy. When supplemented with the 50S subunit, the particles bound tRNA to the 70S P site in a codon- and Mg2+-dependent manner. The specific binding activity was 94% that of particles reconstituted with natural rRNA and 52% that of native 30S. Cross-linking to P site bound tRNA was also preserved. Changing C-1400, the residue known to be close to the anticodon of P site bound tRNA, to A had little effect on reconstitution, but the C----G substitution caused a marked inhibition of assembly. tRNA could bind to both reconstituted mutants, but cross-linking was greatly reduced. These results show that none of the modified bases of 16S RNA are essential for P site binding and that position 1400 may be more important for ribosome assembly than for tRNA binding. Base-specific in vitro mutagenesis can now be used to explore in detail the functional properties of individual residues in ribosomal RNA.

Base Sequence↗
PubMed1986

Computer-averaged views of the 70 S monosome from Escherichia coli.

The prokaryotic (70 S) monosome, composed of a roughly hemispherical 50 S large subunit and an elongate 30 S small subunit, appears in the electron micrograph in only a few common views representing the small number of preferred orientations assumed by the particle. Two of these, termed O and L views, have previously been characterized as the overlap and non-overlap projections; a third view, which we term the R view, represents the other endpoint of a rotational continuum with the overlap or O view. Tilt studies enabled us to calibrate this range as spanning approximately 50 degrees. The disjunct set of L views was averaged, and the reproducible resolution was determined to be 1/3.5 nm-1. The combined sets of O and R views were analyzed by correspondence analysis, and a continuous "rotation series" of subaverages was obtained. Interpretation of the views in the light of what is known about the morphologies of the individual subunits allows a general picture of the mutual fit of the subunits in the monosome to be conceived.

Computers↗
PubMed1985

Investigation of the 50 S ribosomal subunit by electron microscopy and image analysis.

In electron micrographs of 50 S (large) subunits from Escherichia coli ribosomes, the highly preferred crown view is inferred to represent the roughly hemispherical particle lying with its flat or concave face against the carbon film. Single particle averaging allows the reproducible details of the crown view particle to be recognized. Multivariate image analysis shows the most variable morphological features of this view to be the two side protrusions, the L7/L12 stalk and the L1 ridge, both of which show apparent positional variations. The invariance of the features of the particle body implies that the movements of the side protrusions are not merely a result of perspective changes produced by major rotations of the particle body out of its quasistable, flat-lying position. A bending point localized on the L7/L12 stalk is conjectured to represent a functional "hinge" that may be related to the secondary/tertiary structure of the L7/L12 dimeric protein.

Escherichia coli↗
PubMed1985

Bacterial gene expression and biotechnology.

This brief review article has been intended to give a few up-to-date examples of the dramatic impact that our knowledge of gene expression (especially bacterial gene expression) has had in the area of biotechnology. This area is in a state of such rapid growth that it has only been possible to present a limited overview of the subject matter. We have tried to illustrate our points with examples from work in which we have had some direct involvement. It should be apparent that continued increase in our understanding of gene expression should provide additional opportunities for expanded application of the new methodology.

Bacteria↗
PubMed1985

Quantitative structural analysis of eukaryotic ribosomal RNA by scanning transmission electron microscopy.

The conformation of 28S ribosomal RNA isolated from baby hamster kidney cells was studied by scanning transmission electron microscopy (STEM) and circular dichroic spectroscopy to establish the conditions under which STEM images of unstained freeze-dried rRNA are a meaningful representation of the conformation of rRNA in solution. We have determined the conformation of 28S rRNA under various buffer conditions, the molecular mass, the mass distribution, and the number of polynucleotide strands within the individual molecules, and the apparent radii of gyration. The 28S rRNA molecule is highly extended in water and becomes compact with increasing ionic strength. However, even in the "reconstitution buffer" (30 mM Tris/HCl/20 mM MgCl2/360 mM KCl, pH 7.6) the compactness does not reach a state in which the rRNA molecule appears structurally similar to the 60S ribosomal subunit. Our approach has a broad application in high-resolution structural studies of nucleic acids and nucleic acid-protein interactions.

Animals↗
PubMed1984

Three-dimensional reconstruction of the 30 S ribosomal subunit from randomly oriented particles.

Electron micrographs show the small (30 S) subunit of Escherichia coli ribosomes lying in a wide range of positions on the specimen support, related by rotation principally around the long axis of the particle. Through correspondence analysis, a multivariate statistical method that distinguishes the major factors accounting for interimage variance, the (aligned) views of the randomly oriented particles were ordered and grouped according to tilt angle. Views so grouped were then averaged and used as input to a three-dimensional reconstruction program. The particle reconstructed from nine averaged projections spanning a 160 degrees rotational range has a resolution of 5 nm in planes perpendicular to the long axis of the particle and approximately 3 nm in the direction of the long axis. It is somewhat asymmetrical and quite compact; its most conspicuous feature is the "platform" that wraps partially around the middle of the subunit.

Escherichia coli↗
PubMed1984

High resolution localization of the tRNA anticodon interaction site on the Escherichia coli 30 S ribosomal subunit.

A body of previous work has shown that when Escherichia coli tRNAVal1 is placed in the P site of E. coli ribosomes and irradiated, the 5'-anticodon base of this tRNA, 5-carboxymethoxyuridine, is cross-linked to C-1400 of the 16 S rRNA. By tagging the carboxyl group of the cross-linked tRNA residue with a 2,4-dinitrophenyl (DNP) group attached via a 9 A spacer, it has been possible to directly visualize this cross-linking site by immunoelectron microscopy. The DNP group was attached by addition of ethylenediamine to the carboxyl group, followed by condensation of the newly formed free amino group with the N-hydroxysuccinimide ester of N-2,4-dinitrophenyl-gamma-aminobutyric acid. When reacted with anti-DNP antibody, this modification brings the surface of the antibody to within 9 A of the pyrimidine ring which was cross-linked. Neither codon-dependent binding nor cross-linking were materially affected by the tRNA modification. The tRNA-ribosome adduct formed a stable complex with anti-DNP antibody only when 50-30 S subunit association was prevented. Electron microscopic examination of the immune complexes showed that greater than 95% of those detected had the antibody localized deep in the cleft which separates the head and neck of the 30 S from the large protrusion. Since this is the site of cross-linking of the anticodon of tRNA, we conclude that this region on the 30 S subunit corresponds to the decoding site.

Antibodies↗
PubMed1984

Immunoelectron microscopic localization of the S19 site on the 30 S ribosomal subunit which is crosslinked to A site bound transfer RNA.

Phe-tRNA of Escherichia coli, specifically derivatized at the S4U8 position with the 9 A long p-azidophenacyl photoaffinity probe, was crosslinked exclusively to protein S19 of the 30 S ribosomal subunit when the transfer RNA occupied the ribosomal A site (Lin et al., 1983). Two antigenic sites for S19 are known, on opposite sides of the head of the subunit. In this work, discrimination between these two sites was accomplished by affinity immunoelectron microscopy. A dinitrophenyl group was placed on the acp3U47 residue of the same tRNA molecules bearing the photoprobe on S4U8. Addition of this group affected neither aminoacylation, A site binding, nor crosslinking. It also made possible specific affinity purification of crosslinked tRNA-30 S complexes from unreactive 30 S. Reaction of the 2,4-dinitrophenyl-labeled tRNA-30 S complex with antibody was followed by immunoelectron microscopy to reveal the sites of attachment. All of the bound antibody was associated with the ribosome region corresponding to only one of the two known antigenic sites for S19, namely the one closer to the large side projection of the 30 S subunit. A site within this region must be within 10 A of the S4U8 residue of tRNA when it is bound in the ribosomal A site.

Azides↗
PubMed1983

Structure of the lac carrier protein of Escherichia coli.

Circular dichroic measurements on the lac carrier protein purified from the cytoplasmic membrane of Escherichia coli indicate that 85 +/- 5% of the amino acid residues comprising this integral membrane protein are arranged in helical secondary structures. Analysis of the sequential hydropathic character of this protein by the method of Kyte and Doolittle (J. Mol. Biol. (1982) 157, 105-132) indicates that the protein is composed of at least 12 hydrophobic segments with a mean length of 24 +/- 4 residues/segment. Approximately 70% of the 417 amino acids in the lac carrier are found in these domains. The hydropathic profile, together with the circular dichroic measurements, suggest that the 12 hydrophobic segments are largely in a helical conformation. If the segments are assumed to be alpha-helical, the mean length of each domain approximates the thickness of the most hydrophobic portion of the lipid bilayer. Based on these considerations, it is proposed that the lac carrier protein consists of at least 12 alpha-helical segments that traverse the membrane in a perpendicular sense, i.e. in a fashion similar to bacteriorhodopsin.

Circular Dichroism↗
PubMed1983

Electron microscopic study of eukaryotic 40S initiation complex in protein synthesis.

This electron microscopic study demonstrates that formation of a functional eukaryotic 40S initiation complex is accompanied by conformational changes which obscure the characteristic structural features of the 40S ribosomal subunits and of the initiation factor eIF-3, the only macromolecular components of the complex individually resolvable by conventional high resolution electron microscopy. The complex, characterized by a sedimentation coefficient of 46S, appears as a globular particle with a diameter of about 280 A and several characteristic protrusions and incisions. Similar structures were obtained with [40S X eIF-3] initiation complexes formed by interaction of eIF-3 from rabbit reticulocytes with 40S ribosomal subunits from either A. salina cysts or mouse liver. Incubation of eIF-3 with prokaryotic 30S subunits from E. coli produced no [30S X eIF-3] structures. The binding of eIF-3 to 40S subunits is weak, and both the [40S X eIF-3] and the complete 40S initiation complexes have to be stabilized by glutaraldehyde fixation. The extensive conformational changes associated with the complex formation preclude direct electron microscopic localization of eIF-3, a globular protein approximately 100 A in diameter, in the initiation domain of the 40S subunit.

Animals↗
PubMed1982

Electron microscopic study of free and ribosome bound rRNAs from E. coli.

The morphology of ribosomal subunits, nucleoprotein cores, and free rRNAs from Escherichia coli has been studied by two high resolution electron microscopic techniques. Conventional transmission electron micrographs showed unfolding of 30S and 50S ribosomal subunits with increasing depletion of proteins. With dedicated (0.3 nm resolution) scanning transmission electron microscopy we were able to visualize unstained freeze dried ribosomal subunits and free rRNAs without artifacts of staining and structural distortion by air drying. By this technique, we have also determined the mass of individual ribosomal particles and rRNA molecules. While the ribosomal subunits displayed their characteristic structural features and mass, free rRNAs appeared unfolded and polydisperse. These results provide direct evidence for distinct conformational differences between free rRNAs and native ribosomal subunits of E. coli.

Escherichia coli↗
PubMed1981

Computer averaging of electron micrographs of 40S ribosomal subunits.

An enhanced lateral view of the 40S ribosomal subunit of HeLa cells has been obtained by computer averaging of single particles visualized in the electron microscope. Application of crystallographic criteria to independent averages shows that the reproducibility of the result is comparable to that obtained for thin, stained protein crystals by conventional Fourier filtration methods.

Computers↗
PubMed1981

A RNA helix-destabilizing protein is a major component of Artemia salina nuclear ribonucleoproteins.

A major component of 30S heterogeneous nuclear ribonucleoprotein (hnRNP) particles from Artemia salina is HD40, a protein that has been characterized as a RNA helix-destabilizing protein [Marvil, D. K., Nowak, L. & Szer, W. (1980) J. Biol. Chem. 255, 6466-6472; Nowak, L., Marvil, D. K., Thomas, J. O., Boublik, M. & Szer, W. (1980) J. Biol. Chem. 255, 6473-6478]. HD40 binds to and disrupts the secondary structure of nuclear RNA fragments isolated from 30S hnRNP with a stoichiometry of one protein per 10-12 nucleotides. The addition of HD40 in excess of this ratio results in the formation of bead-like HD4-nuclear RNA complexes that are similar in properties and appearance to native 30S hnRNP particles. The heterogeneous nuclear RNA (hnRNA) in the HD40-hnRNA complexes is unstacked and unfolded to about the same extent as the RNA in the native 30S hnRNP particles. HD40 is strikingly similar in molecular weight (40,000) and amino acid composition (no cysteine, high glycine, presence of dimethylarginine, and blocked NH2 terminus) to eukaryotic hnRNP proteins isolated from many cell types. HD40 can be separated into three isoelectric species with basic pIs, which appears to be posttranslational modifications of a single polypeptide chain.

Animals↗
PubMed1980

A single-stranded nucleic acid-binding protein from Artemia salina. II. Interaction with nucleic acids.

A helix-destabilizing protein, HD40 (Mr 40,000), isolated from the cytoplasm of Artemia salina (Marvil, D.K., Nowak, L., and Szer, W. (1980) J. Biol. Chem. 255, 6466-6472) stoichiometrically disrupts the secondary structures of synthetic single-stranded and helical polynucleotides (e.g. poly(rA), poly(dA), poly(rC), poly(dC), and poly(rU)) as well as those of natural polynucleotides (e.g. MS2 RNA and phi X174 viral DNA). The conformations of double-stranded DNA and double- or triple-stranded synthetic polynucleotides are not affected by the protein. Formation of duplexes, e.g. poly(rA . rU), is prevented by HD40 at 25 to 50 mM but not at 100 to 140 mM NaCl. The unwinding of the residual secondary structure of RNA and DNA by HD40 is not highly cooperative and has a stoichiometry of one HD40 per 12 to 15 nucleotides. The addition of HD40 in excess of 1 molecule per 12 to 15 nucleotides results in the cooperative formation of distinct bead-like structures along the nucleic acid strand. The beads are about 20 nm in diameter with a center to center distance of about 40 nm. The appearance of the beads is not accompanied by any spectral changes (CD and UV) beyond those obtained at a stoichiometry of one HD40 molecule per 12 to 15 nucleotides.

Animals↗
PubMed1980

Conformation of ribosomes from the vegetative amoebae and spores of Dictyoistelium discoideum.

Ribosomes from two different cell types of D. discoideum--the undifferentiated amoebae and the differentiated spores--display considerable differences in protein composition (Ramagopal and Ennis 1979 and manuscript in preparation). These differences do not affect the three-dimensional structure of monosomes and large (60S) and small (40S) subunits from the two cell types to an extent detectable by sedimentation analysis or electron microscopy. High resolution electron microscopic images of ribosomal particles from the amoebae and the spores are similar and, in general, comparable to that of 80S, 60S, and 40S ribosomal particles from other eukaryotic sources. However, distinct differences in the conformation and stability of the two types of ribosomes are detectable by circular dichroic spectroscopy. The degree of the ordered secondary structure of rRNAs is similar in the 80S monosomes from the amoebae and the spores, but higher in the amoeba subunits. The results of thermal melting experiments show that the small subunit from the spores is more stable than that from the amoebae. The established differences in the conformation of rRNAs, most probably due to the interactions with cell-specific ribosomal proteins, can be responsible for the differences in stability of ribosomes from the two cell types of slime mold.

Cell Cycle↗