scholarly journals Structure and functions of 5S rRNA.

2001 ◽  
Vol 48 (1) ◽  
pp. 191-198 ◽  
Author(s):  
M Z Barciszewska ◽  
M Szymański ◽  
V A Erdmann ◽  
J Barciszewski
Keyword(s):  
Messenger Rna ◽  
Protein Biosynthesis ◽  
Large Subunit ◽  
Genetic Material ◽  
Ribosomal Subunit ◽  
Peptide Bond ◽  
Small Subunit ◽  
5S Rrna ◽  
23S Rrna ◽  
Peptide Bond Formation

The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all organisms. It is composed of two-subunit, ribonucleoprotein particles that translate the genetic material into an encoded polypeptides. The small subunit is the site of codon-anticodon interaction between the messenger RNA (mRNA) and transfer RNA (tRNA) substrates, and the large subunit catalyses peptide bond formation. The peptidyltransferase activity is fulfilled by 23S rRNA, which means that ribosome is a ribozyme. 5S rRNA is a conserved component of the large ribosomal subunit that is thought to enhance protein synthesis by stabilizing ribosome structure. This paper shortly summarises new results obtained on the structure and function of 5S rRNA.

scholarly journals Ribosome Biogenesis in African Trypanosomes Requires Conserved and Trypanosome-Specific Factors

2014 ◽  
Vol 13 (6) ◽  
pp. 727-737 ◽  
Author(s):  
Khan Umaer ◽  
Martin Ciganda ◽  
Noreen Williams
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
5S Rrna ◽  
Content Type ◽  
African Trypanosomes ◽  
Ribosomal Protein L5

ABSTRACTLarge ribosomal subunit protein L5 is responsible for the stability and trafficking of 5S rRNA to the site of eukaryotic ribosomal assembly. InTrypanosoma brucei, in addition to L5, trypanosome-specific proteins P34 and P37 also participate in this process. These two essential proteins form a novel preribosomal particle through interactions with both the ribosomal protein L5 and 5S rRNA. We have generated a procyclic L5 RNA interference cell line and found that L5 itself is a protein essential for trypanosome growth, despite the presence of other 5S rRNA binding proteins. Loss of L5 decreases the levels of all large-subunit rRNAs, 25/28S, 5.8S, and 5S rRNAs, but does not alter small-subunit 18S rRNA. Depletion of L5 specifically reduced the levels of the other large ribosomal proteins, L3 and L11, whereas the steady-state levels of the mRNA for these proteins were increased. L5-knockdown cells showed an increase in the 40S ribosomal subunit and a loss of the 60S ribosomal subunits, 80S monosomes, and polysomes. In addition, L5 was involved in the processing and maturation of precursor rRNAs. Analysis of polysomal fractions revealed that unprocessed rRNA intermediates accumulate in the ribosome when L5 is depleted. Although we previously found that the loss of P34 and P37 does not result in a change in the levels of L5, the loss of L5 resulted in an increase of P34 and P37 proteins, suggesting the presence of a compensatory feedback loop. This study demonstrates that ribosomal protein L5 has conserved functions, in addition to nonconserved trypanosome-specific features, which could be targeted for drug intervention.

Depletion and Reconstitution of Active E. Coli Ribosomes

1975 ◽  
Vol 33 ◽  
pp. 640-641
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Protein Biosynthesis ◽  
Large Subunit ◽  
High Resolution Electron Microscopy ◽  
Small Subunit ◽  
Structure And Function ◽  
Biologically Active ◽  
Biological Macromolecules ◽  
E Coli ◽  
Resolution Electron ◽  
And Function

Correlations between structure and function of biological macromolecules have been studied intensively for many years, mostly by indirect methods. High resolution electron microscopy is a unique tool which can provide such information directly by comparing the conformation of biopolymers in their biologically active and inactive state. We have correlated the structure and function of ribosomes, ribonucleoprotein particles which are the site of protein biosynthesis. 70S E. coli ribosomes, used in this experiment, are composed of two subunits - large (50S) and small (30S). The large subunit consists of 34 proteins and two different ribonucleic acid molecules. The small subunit contains 21 proteins and one RNA molecule. All proteins (with the exception of L7 and L12) are present in one copy per ribosome.This study deals with the changes in the fine structure of E. coli ribosomes depleted of proteins L7 and L12. These proteins are unique in many aspects.

scholarly journals Crystal structure of eukaryotic ribosome and its complexes with inhibitors

2017 ◽  
Vol 372 (1716) ◽  
pp. 20160184 ◽  
Author(s):  
Gulnara Yusupova ◽  
Marat Yusupov
Keyword(s):  
Crystal Structure ◽  
Ribosomal Rna ◽  
Protein Biosynthesis ◽  
Protein Translation ◽  
Peptide Bond ◽  
Binding Mode ◽  
High Eukaryote ◽  
Peptide Bond Formation ◽  
80S Ribosome ◽  
Eukaryotic Ribosome

A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome—the high-eukaryote–specific long ribosomal RNA segments (about 1MDa)—remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved. This article is part of the themed issue ‘Perspectives on the ribosome’.

Purification of factor EF-P, a protein that stimulates peptide-bond synthesis with certain aminoacyl-tRNA analogues

1979 ◽  
Vol 57 (6) ◽  
pp. 749-757 ◽  
Author(s):  
Bernard R. Glick ◽  
Robert M. Green ◽  
M. Clelia Ganoza
Keyword(s):  
Escherichia Coli ◽  
Molecular Weight ◽  
Protein Biosynthesis ◽  
Bond Formation ◽  
Frictional Coefficient ◽  
Peptide Bond ◽  
Asymmetric Structure ◽  
Peptide Bond Formation ◽  
Apparent Homogeneity ◽  
Stokes Radius

Factor EF-P is a nonribosomal (soluble) protein of Escherichia coli that stimulates peptide bond synthesis when certain aminoacyl-tRNA analogues are used. The purification of this protein to apparent homogeneity is described here. EF-P has a molecular weight of about 21 000, a Stokes radius of 27 Å (1 Å = 0.1 nm), and a frictional coefficient of 1.48, suggesting an asymmetric structure. By this and a number of other criteria, EF-P is a new factor that controls peptide bond formation during protein biosynthesis.

scholarly journals Retapamulin Inhibition of Translation and 50S Ribosomal Subunit Formation in Staphylococcus aureus Cells

2007 ◽  
Vol 51 (9) ◽  
pp. 3385-3387 ◽  
Author(s):  
W. Scott Champney ◽  
Ward K. Rodgers
Keyword(s):  
Staphylococcus Aureus ◽  
16S Rrna ◽  
Cell Viability ◽  
Protein Biosynthesis ◽  
Ribosomal Subunit ◽  
Inhibitory Effect ◽  
23S Rrna ◽  
Specific Inhibition ◽  
Methicillin Resistant

ABSTRACT Retapamulin inhibited protein biosynthesis and cell viability in methicillin-sensitive and methicillin-resistant Staphylococcus aureus organisms. A specific inhibitory effect on 50S ribosomal subunit formation was also found. Pulse-chase labeling experiments confirmed the specific inhibition of 50S subunit biogenesis. Turnover of 23S rRNA was found, with no effect on 16S rRNA amounts.

scholarly journals Changes in Ribosomal Activity of Escherichia coli Cells during Prolonged Culture in Sea Salts Medium

1998 ◽  
Vol 180 (12) ◽  
pp. 3114-3119 ◽  
Author(s):  
Dimitrios L. Kalpaxis ◽  
Panagiotis Karahalios ◽  
M. Papapetropoulou
Keyword(s):  
Escherichia Coli ◽  
Initial Phase ◽  
Peptide Bond ◽  
Molar Ratio ◽  
23S Rrna ◽  
Logarithmic Phase ◽  
Starvation Period ◽  
Peptide Bond Formation ◽  
Sea Salts ◽  
Catalytic Rate Constant

ABSTRACT The activity of ribosomes from a clinical isolate ofEscherichia coli, exposed to starvation for 7 days in sea salts medium, was investigated by measuring the kinetic parameters of ribosomal peptidyltransferase, by using the puromycin reaction as a model reaction. No alterations in the extent of peptide bond formation were observed during starvation. In contrast, a 50% reduction in thek max/Ks ratio could be seen after 24 h of starvation; an additional 6 days of starvation resulted in a progressive but less abrupt decline in thek max/Ks value. {k max is the apparent catalytic rate constant of peptidyl transferase, and Ks is the dissociation constant of the encounter complex between acetyl (Ac)[3H]Phe-tRNA-poly(U)-ribosome and puromycin.} Although the distribution of ribosomal particles remained constant, a substantial decrease in the number of ribosomes per starved cell and a clear decline in the ability of ribosomes to bind AcPhe-tRNA were observed, particularly during the first day of starvation. Further analysis indicated that rRNA in general, but especially 23S rRNA, was rapidly degraded during the starvation period. In addition, the L12/L7 molar ratio decreased from 1.5 to 1 during the initial phase of starvation (up to 24 h) but remained constant during the subsequent starvation period. Ribosomes isolated from 24-h-starved cells, when artificially depleted of L7/L12 protein and reconstituted with L7/L12 protein from mid-logarithmic-phase cells, regenerated an L12/L7 molar ratio of 1.5 and restored the peptidyltransferase activity to a substantial level. An analogous effect of reconstitution on the efficiency of ribosomes in binding AcPhe-tRNA was evident not only during the initial phase but throughout the starvation period.

scholarly journals Orthoformimycin inhibits translation elongation by displacing the A-site tRNA and preventing peptide bond formation

2021 ◽  
Author(s):  
Andreas Schedlbauer ◽  
Tatsuya Kaminishi ◽  
Attilio Fabbretti ◽  
Pohl Milon ◽  
Xu Han ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Peptide Bond ◽  
Resistance Mechanisms ◽  
Peptide Bond Formation ◽  
Translation Elongation ◽  
X Ray Crystallography ◽  
Steady State Kinetics ◽  
A Site ◽  
Insight Into ◽  
Major Target

The ribosome is a major target for antibiotics owing to its essential cellular role in protein synthesis. Structural analysis of ribosome-antibiotic complexes provides insight into the molecular basis for their inhibitory action and highlights possible avenues to improve their potential or overcome existing resistance mechanisms. Here we use X-ray crystallography and pre-steady state kinetics to detail the inhibitory mechanism of the antimicrobial on the large ribosomal subunit.

scholarly journals A conserved secondary structural motif in 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide bond formation.

1994 ◽  
Vol 13 (7) ◽  
pp. 1682-1686 ◽  
Author(s):  
I.G. Leviev ◽  
C. Rodriguez-Fonseca ◽  
H. Phan ◽  
R.A. Garrett ◽  
G. Heilek ◽  
...  
Keyword(s):  
Bond Formation ◽  
Peptide Bond ◽  
Structural Motif ◽  
23S Rrna ◽  
Peptide Bond Formation

Three-Dimensional Image Reconstruction of the 50S Subunit from Escherichia Coli Ribosomes Lacking 5S-rRNA

1990 ◽  
Vol 48 (1) ◽  
pp. 284-285
Author(s):  
Michael Radermacher ◽  
Volker Nowotny ◽  
Robert Grassucci ◽  
Joachim Frank
Keyword(s):  
Three Dimensional ◽  
Ribosomal Subunit ◽  
5S Rrna ◽  
Scattering Data ◽  
23S Rrna ◽  
Reconstruction Technique ◽  
Electron Dose ◽  
E Coli ◽  
Phenol Extraction ◽  
Negative Stain

In earlier studies the structure of the 50S ribosomal subunit from E. coli has been determined from electron micrographs, using the single exposure random conical reconstruction technique. For the understanding of the function of ribosomes the single proteins and ribosomal RNAs need to be located within the ribosome structure. For localization of most proteins immunoelectron microscopy and neutron scattering data are available. The current study’s goal is the localization of the 5S rRNA from a comparison of the structures of complete 50S subunits with that of subunits reconstituted omitting the 5S rRNA.By Phenol extraction of purified 50S subunits the rRNA fraction was separated form the total protein fraction (TP50). This rRNA fraction was separated into 23S rRNA and 5S rRNA via HPLC on a DEAE-column. The total reconstitution of 23S rRNA and the equivalent amount of TP50 resulted in particles lacking the 5S rRNA. For electron microscopy the subunits were prepared in a negative stain sandwich preparation.Twenty tilt pairs at 50° tilt and 0° were recorded, with an electron dose of approximately 10el/A2 and a magnification of 49,000. A total of 983 particles were selected from these data. The 0° images were aligned using the procedure described in.

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