scholarly journals Terminal-sequence studies of high-molecular-weight ribonucleic acid. The 3′-termini of rabbit reticulocyte ribosomal ribonucleic acid

1970 ◽  
Vol 120 (2) ◽  
pp. 353-363 ◽  
Author(s):  
John A. Hunt
Keyword(s):  
Ribonucleic Acid ◽  
Periodate Oxidation ◽  
Ribosomal Subunit ◽  
Large Ribosomal Subunit ◽  
Terminal Sequence ◽  
Ribosomal Subunits ◽  
Rna Molecules ◽  
Ribosomal Ribonucleic Acid ◽  
Rabbit Reticulocytes

Sequences of the polynucleotide chains of RNA found in the large and small ribosomal subunits of rabbit reticulocytes have been determined from the 3′-end by use of periodate oxidation and condensation with [3H]isoniazid and by stepwise degradation. By these methods the hexanucleotide sequences have been found as -pGpUpUpUpGpU for the 28S RNA and -pGpUpCpGpCpU for the 6S RNA of the large ribosomal subunit and the octanucleotide sequence -pGpApUpCpApUpUpA for the 18S rRNA of the small ribosomal subunit. These sequences are present in at least 70% of all the RNA molecules and are discussed in relation to the specific cleavage of rRNA from its precursors and the role of multiple cistrons for rRNA in the DNA of higher organisms. The feasibility of using the method for longer sequence determinations is discussed.

Three-dimensional reconstruction of the 40S ribosomal subunit from rabbit reticulocytes

1987 ◽  
Vol 45 ◽  
pp. 936-937
Author(s):  
Neng-Yu Zhang ◽  
Terence Wagenknecht ◽  
Michael Radermacher ◽  
Tom Obrig ◽  
Joachim Frank
Keyword(s):  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Uranyl Acetate ◽  
Reconstruction Method ◽  
Single Exposure ◽  
Electron Dose ◽  
Ribosomal Subunits ◽  
40S Ribosomal Subunit ◽  
Dimensional Reconstruction ◽  
Rabbit Reticulocytes

We have reconstructed the 40S ribosomal subunit at a resolution of 4 nm using the single-exposure pseudo-conical reconstruction method of Radermacher et al.Small (40S) ribosomal subunits were Isolated from rabbit reticulocytes, applied to grids and negatively stained (0.5% uranyl acetate) in a manner that “sandwiches” the specimen between two layers of carbon. Regions of the grid exhibiting uniform and thick staining were identified and photographed twice (magnification 49,000X). The first micrograph was always taken with the specimen tilted by 50° and the second was of the Identical area untilted (Fig. 1). For each of the micrographs the specimen was subjected to an electron dose of 2000-3000 el/nm2.Three hundred thirty particles appearing in the L view (defined in [4]) were selected from both tilted- and untilted-specimen micrographs. The untilted particles were aligned and their rotational alignment produced the azimuthal angles of the tilted particles in the conical tilt series.

scholarly journals Role of conformational heterogeneity in ligand recognition by viral RNA molecules

2021 ◽  
Author(s):  
Lev Levintov ◽  
Harish Vashisth
Keyword(s):  
Conformational Changes ◽  
Ribonucleic Acid ◽  
Viral Rna ◽  
Ligand Recognition ◽  
Conformational Heterogeneity ◽  
Rna Molecules ◽  
Environmental Stimuli

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example...

scholarly journals Identical 3′-terminal octanucleotide sequence in 18S ribosomal ribonucleic acid from different eukaryotes. A proposed role for this sequence in the recognition of terminator codons

1974 ◽  
Vol 141 (3) ◽  
pp. 609-615 ◽  
Author(s):  
John Shine ◽  
Lynn Dalgarno
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Synthesis ◽  
Drosophila Melanogaster ◽  
Ribosomal Rna ◽  
Ribonucleic Acid ◽  
18S Rrna ◽  
Base Sequence ◽  
Terminal Sequence ◽  
Ribosomal Ribonucleic Acid ◽  
Rrna Species

The 3′-terminal sequence of 18S ribosomal RNA from Drosophila melanogaster and Saccharomyces cerevisiae was determined by stepwise degradation from the 3′-terminus and labelling with [3H]isoniazid. The sequence G-A-U-C-A-U-U-AOH was found at the 3′-terminus of both 18S rRNA species. Less extensive data for 18S RNA from a number of other eukaryotes are consistent with the same 3′-terminal sequence, and an identical sequence has previously been reported for the 3′-end of rabbit reticulocyte 18S rRNA (Hunt, 1970). These results suggest that the base sequence in this region is strongly conserved and may be identical in all eukaryotes. As the 3′-terminal hexanucleotide is complementary to eukaryotic terminator codons we discuss the possibility that the 3′-end of 18S rRNA may have a direct base-pairing role in the termination of protein synthesis.

scholarly journals The enigmatic ribosomal stalk

2018 ◽  
Vol 51 ◽  
Author(s):  
Anders Liljas ◽  
Suparna Sanyal
Keyword(s):  
Early Phase ◽  
Ribosomal Subunit ◽  
Structure And Function ◽  
Large Ribosomal Subunit ◽  
Translation Factors ◽  
Ribosomal Stalk ◽  
And Function ◽  
High Degree

Abstract The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding. In this review we summarise the knowhow about the structure and function of the ribosomal stalk till date starting from the early phase of ribosome research.

The ribosomes of Plasmodium berghei: isolation and ribosomal ribonucleic acid analysis

Parasitology ◽  
1978 ◽  
Vol 77 (3) ◽  
pp. 345-366 ◽  
Author(s):  
F. W. Miller ◽  
Judith Ilan
Keyword(s):  
Plasmodium Berghei ◽  
Ribonucleic Acid ◽  
Ribosomal Subunit ◽  
High Yield ◽  
Small Component ◽  
40S Ribosomal Subunit ◽  
Ribosomal Ribonucleic Acid ◽  
Rrna Species ◽  
Specific Degradation ◽  
Triton X

SummaryRibosomes and high molecular weight ribosomal ribonucleic acid (rRNA) from the blood stages of Plasmodium berghei parasites were studied in preparations free from host ribosome contamination. Purified malarial ribosomes were isolated in high yield from a population of ultrastructurally intact, viable parasites by hypertonic lysis with Triton X-100 and differential centrifugation. These ribosomes were shown to be derived from active polysomes and could be dissociated into subunits by puromycin–0·5 m KCl treatment. Malarial rRNA extracted from purified 40S and 60S ribosomal subunits was characterized by electrophoretic, sedimentation and base ratio analyses. Like certain other protozoa, the P. berghei 40S ribosomal subunit possessed an exceptionally large RNA species (mol. wt 0·9 × 106), while RNA isolated from the parasite's 60S subunit (mol. wt 1·5 × 106) was specifically ‘nicked’ to produce one large component (mol.wt 1·2 × 106) and one small component (mol.wt 0·3 × 106) in equimolar quantities. These rRNA's migrate identically on polyacrylamide gels after heating to 63°C for 5 mm or under denaturing conditions in the presence of formamide, indicating an absence of aggregation and non-specific degradation of the rRNA species. Base composition studies showed P. berghei rRNA to be low in guanosine and cytosine content, as is the case for protozoa generally.

Cryo-EM structure of 90S small ribosomal subunit precursors in transition states

Science ◽  
2020 ◽  
Vol 369 (6510) ◽  
pp. 1477-1481 ◽  
Author(s):  
Yifei Du ◽  
Weidong An ◽  
Xing Zhu ◽  
Qi Sun ◽  
Jia Qi ◽  
...  
Keyword(s):  
Structural Changes ◽  
Critical Role ◽  
Ribosomal Subunit ◽  
Rna Degradation ◽  
Ribosomal Subunits ◽  
Cryo Electron Microscopy ◽  
Nuclear Exosome ◽  
Assembly Intermediate ◽  
Insight Into

The 90S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40S ribosome. Here, we gained insight into this transition by determining cryo–electron microscopy structures of Saccharomyces cerevisiae intermediates in the path from the 90S to the pre-40S. The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5′ external transcribed spacer (5′ ETS) is degraded within 90S, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90S through helicase Mtr4 and is primed to digest the 3′ end of the 5′ ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5′ ETS degradation in 90S progression.

What we have learned from ribosome structures

2008 ◽  
Vol 36 (4) ◽  
pp. 567-574 ◽  
Author(s):  
V. Ramakrishnan
Keyword(s):  
High Resolution ◽  
Ribosomal Subunit ◽  
Ribosomal Subunits ◽  
30S Subunit ◽  
High Resolution Structure ◽  
70S Ribosome ◽  
Year 2000 ◽  
Resolution Structure

The determination of the high-resolution structures of ribosomal subunits in the year 2000 and of the entire ribosome a few years later are revolutionizing our understanding of the role of the ribosome in translation. In the present article, I summarize the main contributions from our laboratory to this worldwide effort. These include the determination of the structure of the 30S ribosomal subunit and its complexes with antibiotics, the role of the 30S subunit in decoding, and the high-resolution structure of the entire 70S ribosome complexed with mRNA and tRNA.

scholarly journals Deoxyribonucleic acid–ribonucleic acid hybridization. Annealing and quantitative recovery of intact ribosomal ribonucleic acid molecules from hybrids

1969 ◽  
Vol 115 (2) ◽  
pp. 287-294 ◽  
Author(s):  
Michael Fry ◽  
Michael Artman
Keyword(s):  
Ribosomal Rna ◽  
Ribonucleic Acid ◽  
Messenger Rna ◽  
Deoxyribonucleic Acid ◽  
Cellulose Nitrate ◽  
Absolute Size ◽  
Rna Molecules ◽  
Membrane Filters ◽  
Ribosomal Ribonucleic Acid

A simple and efficient method for hybridization and subsequent recovery of non-fragmented ribosomal RNA from the hybrid is described. The procedure involves annealing of immobilized denatured DNA bound on cellulose nitrate membrane filters to complementary RNA in 50% (v/v) formamide–0·33m-potassium chloride–10mm-tris–hydrochloric acid buffer, pH7·4, at 33° for 3hr. Under these conditions no detectable changes in the sedimentation coefficients of the input RNA were detected. The RNA can subsequently be recovered quantitatively from the hybrid in intact form by incubating the filters in formamide or in 85% (v/v) dimethyl sulphoxide. The applicability of the method for the evaluation of the absolute size of ribosomal RNA cistrons in Escherichia coli DNA and for the determination of the size of messenger RNA molecules is discussed.

scholarly journals Heat-sensitive mutant strain of Neurospora crassa, 4M(t), conditionally defective in 25S ribosomal ribonucleic acid production.

1981 ◽  
Vol 1 (3) ◽  
pp. 199-207 ◽  
Author(s):  
M W Loo ◽  
N S Schricker ◽  
P J Russell
Keyword(s):  
Neurospora Crassa ◽  
Mutant Strain ◽  
Ribosomal Rna ◽  
Ribonucleic Acid ◽  
Ribosomal Subunit ◽  
Macromolecular Synthesis ◽  
Sensitive Mutant ◽  
Ribosomal Subunits ◽  
Sequence Of Events ◽  
Ribosomal Rna Processing

A heat-sensitive mutant strain of Neurospora crassa, 4M(t), was studied in an attempt to define its molecular lesion. The mutant strain is inhibited in conidial germination and mycelial extension at the nonpermissive temperature (37 degrees C). Macromolecular synthesis studies showed that both ribonucleic acid (RNA) and protein syntheses are inhibited when 4-h cultures are shifted from 20 to 37 degrees C. Density gradient analysis of ribosomal subunits made at 37 degrees C indicated that strain 4M(t) is deficient in the accumulation of 60S ribosomal subunits in that the ratio of 60S/37S subunits was 0.29:1 compared with 1.6:1 for the parental strain. This phenotype was shown to be the result of a slow rate of processing of, and a deficiency in the amount of, the immediate precursor to 25S ribosomal RNA (the large RNA of the 60S subunit) in the sequence of events constituting the production of mature ribosomal RNAs from the primary transcript of the ribosomal deoxyribonucleic acid, the precursor ribosomal RNA molecule. Analysis of polysomes suggested that the heat-sensitive gene product might function in both the assembly and the function of the 60S ribosomal subunit, since there was a smaller proportion of newly made 60S subunits synthesized at 37 degrees C in the polysome region of the gradients than in the monosome-plus-subunit region. The ribosomal RNA processing defect is apparently responsible for the observed defects in germination and macromolecular synthesis at 37 degrees C, but the precise molecular lesion is not known. On the basis of these results, the heat-sensitive mutant allele in the 4M(t) strain is considered to define the rip1 (ribosome production) gene locus.

scholarly journals Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit

2019 ◽  
Author(s):  
Christina M Braun ◽  
Philipp Hackert ◽  
Catharina E Schmid ◽  
Markus T Bohnsack ◽  
Katherine E Bohnsack ◽  
...  
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Large Ribosomal Subunit ◽  
Rrna Sequence ◽  
Ribosomal Subunits ◽  
External Transcribed Spacer ◽  
Exit Tunnel ◽  
Domain Iii

Abstract More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5′ external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5′ ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.

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