[40] The inactivation and reactivation of Escherichia coli ribosomes

Zamir, Ada; Miskin, Ruth; Vogel, Zvi; Elson, David

doi:10.1016/0076-6879(74)30042-0

Cited by 90 publications

(63 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…11,41 Despite the PTC high conservation, variability of its conformation resulting from alterations of parameters such pH, temperature and ion concentration, has been suggested, based on biochemical findings, over three decades ago. [42][43][44] These observations were confirmed recently by several methods, including chemical probing 45 and cryo-electron microscopy studies, investigating the effect of buffer composition on tRNA-ribosome interactons. 46 Consistently, conformational differences were observed by comparing the available crystal structures that were determined under various conditions.…”

Section: Regulation Discrimination and Signaling Subunit Associationsupporting

confidence: 49%

Functional aspects of ribosomal architecture: symmetry, chirality and regulation

Zarivach

Bashan

Berisio

et al. 2004

J of Physical Organic Chem

View full text Add to dashboard Cite

High-resolution structures of both ribosomal subunits revealed that most stages of protein biosynthesis, including decoding of genetic information, are navigated and controlled by the elaborate ribosomal architecturaldesign. Remote interactions govern accurate substrate alignment within a flexible active-site pocket [peptidyl transferase center (PTC)], and spatial considerations, due mainly to a universal mobile nucleotide, U2585, ensure proper chirality by interfering with D-amino-acids incorporation. tRNA translocation involves two correlated motions: overall mRNA/tRNA (messenger and transfer RNA) shift, and a rotation of the tRNA single-stranded aminoacylated-3 0 end around the bond connecting it with the tRNA helical-regions. This bond coincides with an axis passing through a sizable symmetry-related region, identified around the PTC in all large-subunit crystal structures. Propelled by a bulged universal nucleotide, A2602, positioned at the two-fold symmetry axis, and guided by a ribosomal-RNA scaffold along an exact pattern, the rotatory motion results in stereochemistry optimal for peptide-bond formation and in geometry ensuring nascent proteins entrance into their exit tunnel. Hence, confirming that ribosomes contribute positional rather than chemical catalysis, and that peptide bond formation is concurrent with A-to P-site tRNA passage. Connecting between the PTC, the decoding center, the tRNA entrance and exit points, the symmetry-related region can transfer intra-ribosomal signals between remote functional locations, guaranteeing smooth processivity of amino acids polymerization. Ribosomal proteins are involved in accurate substrate placement (L16), discrimination and signal transmission (L22) and protein biosynthesis regulation (CTC). Residing on the exit tunnel walls near its entrance, and stretching to its opening, protein-L22 can mediate ribosome response to cellular regulatory signals, since it can swing across the tunnel, causing gating and elongation arrest. Each of the protein CTC domains has a defined task. The N-terminal domain stabilizes the intersubunit-bridge confining the A-site-tRNA entrance. The middle domain protects the bridge conformation at elevated temperatures. The C-terminal domain can undergo substantial conformational rearrangements upon substrate binding, indicating CTC participation in biosynthesiscontrol under stressful conditions.

show abstract

Section: Regulation Discrimination and Signaling Subunit Associationsupporting

confidence: 49%

Functional aspects of ribosomal architecture: symmetry, chirality and regulation

Zarivach

Bashan

Berisio

et al. 2004

J of Physical Organic Chem

View full text Add to dashboard Cite

show abstract

“…Although under these conditions the ribosomes are dissociated into subunits, they are referred to as inactive 70-S ribosomes. Inactive 70-S ribosomes were fully activated as described [2]. It should, however, be emphasized, that only about 30% of those ribosomes were active in initiation complex formation with poly(A,U,G) and in the nonenzymic binding of phenylalanine in the presence of poly(U).…”

Section: Ribosomesmentioning

confidence: 93%

“…In principle the depletion of certain monovalent cations from the medium inactivates both ribosomal subunits, and the 30-S subunit is also inactivated at reduced magnesium concentrations. In all cases activity can be fully or partially restored by heating the inactive ribosomes in appropriate media [ 1,2].…”

mentioning

confidence: 99%

“…The factor differs by several criteria from the known initiation, elongation and termination factors and also from ribosomal proteins of the 30-S subunit. Since active and inactive 30-S subunits clearly differ in their conformation [2,3], it is likely that the stimulatory effect exerted by the factor on the transition from the inactive to the active state is related to its ability to affect ribosomal conformation.…”

mentioning

confidence: 99%

See 1 more Smart Citation

A Protein Factor Enhancing Activation of Inactive 30‐S Ribosomal Subunits of Escherichia coli

Miskin

1976

European Journal of Biochemistry

Self Cite

View full text Add to dashboard Cite

A protein factor partially purified from the S‐100 fraction (supernatant from 100000 × g spin) of Escherichia coli stimulates the conversion of 30‐S ribosomal subunits from an inactive to an active form. The subunits are normally inactivated at low concentrations of Mg2+ and reactivated when heated under appropriate ionic conditions. The factor, which differs from the known soluble factors required for protein biosynthesis as well as from proteins of the 30‐S subunit, enhances activation under conditions which by themselves allow for only a low level of activity to reappear. Fully active ribosomes and the assay reactions are not affected by the factor, indicating that its effect must be restricted to the activation process. The factor is likely to function by facilitating a conformational transition in the ribosome, and might act in vivo in a similar manner

show abstract

“…. 30-S subunits were activated as described by Zamir et al [37], dialyzed against buffer A, divided in small portions and stored at -50 "C. Before use the 30-S subunits were preheated in buffer A at 37 "C for 10-15 min. 1 mol of 30-S subunits was able to bind not less than 0.7 mol Phe-tRNA in the poly(U)-dependent system.…”

Section: -S Subunits Of E Coli Ribosomes Form Complexes Withmentioning

confidence: 99%

Proteins of the 30‐S Subunit of Escherichia coli Ribosomes which Interact Directly with Natural mRNA

Broude

Kussova

Mecvedeva

et al. 1983

European Journal of Biochemistry

View full text Add to dashboard Cite

Ultraviolet irradiation (254 nm) of the complexes of MS2 phage RNA (mRNA) and the 30-S subunits of E.sclzeviclzia coli ribosomes prepared at 0 'C and 37 'C in the presence and absence of initiation factor 3 (IF-3) causes cross-linking of mRNA with proteins S3, S4, S5, S7, S9, S18 and IF-3. Hence, these proteins interact directly with mRNA within the complex 30-S-subunit . mRNA.Addition of IF-3 results in an increase of the rate of complex formation and decrease of its dissociation rate. The addition of IF-3 changes the relative amounts of cross-linked proteins (mainly S3, S4 and S18).Decreasing the temperature from 37 'C to 0 "C not only decelerates the complex formation rate but also changes the relative amount of cross-linked proteins, indicating the influence of the conditions on the structure of the complex.It is well known that prokaryotic messenger RNAs are polycistronic and initiation can take place at the internal sites of the RNA [I]. The selection of initiation sites in messenger RNA depends on RNA conformation ; therefore unfolding of RNA allows the ribosome to interact with additional AUG codons [2,3]. On the other hand, the specificity of initiation is determined by the ribosome itself. For instance, ribosomes of Bacillus stearothermophilus translate predominantly the A protein on RNAs of phages R17 and f 2 [2,4] , whereasEscherichia coli ribosomes translate the coat protein on the same messengers [2].Up to now, the only known molecular interactions involved in initiation complex formation are Shine-Dalgarno interactions, i.e. the complementary binding of the nucleotide sequence near the 3' end of 16-S rRNA and the region in messenger RNA 5'-distal to the initiation codon [S]. However, it has been shown that E. coli ribosomes are able to translate messenger RNAs which do not contain the ShineDalgarno sequence [6]. At the same time eukaryotic ribosomes which possess no polypyrimidine sequence near the 3' end of 1 6 3 RNA [7] also translate RNA from phages giving rise to the same proteins as E. coli ribosomes [8-101. That implies that the initiation complex stabilisation leading to specific interaction between ribosones and messenger RNA depends on a multiplicity of interactions between the respective sites of mRNA and ribosomal components, the relative role of which can change depending on the ribosome and cistron structure. Therefore the structural study of messenger RNA and ribosomal components involved in initiation complex formation is a prerequisite for understanding the principles of initiation. ~~Abhreviarions. Poly(U), poly(uridy1ic acid); poly(s4U), poly(4-thiouridylic acid); IF-3, initiation factor 3 ; rRNA, ribosomal R N A ; 3 0 s . MS2 RNA, complex between 3 0 3 subunits and MS2 RNA; 3 0 3 IF3 . MS2 RNA, complex containing 30-S subunits, IF-3 and MS2 RNA.En;-vmrs. RNase A (EC 3.1.27.5); RNase TI (EC 3.1.27.3); alkaline phosphatase (EC 3.1.3.1); polynucleotide kinase (EC 2.7.1.78). 30-S subunits of E. coli ribosomes form complexes withRNAs from phages in the absence of initiator tRNA [I 1 ...

show abstract

[40] The inactivation and reactivation of Escherichia coli ribosomes

Cited by 90 publications

References 21 publications

Functional aspects of ribosomal architecture: symmetry, chirality and regulation

Functional aspects of ribosomal architecture: symmetry, chirality and regulation

A Protein Factor Enhancing Activation of Inactive 30‐S Ribosomal Subunits of Escherichia coli

Proteins of the 30‐S Subunit of Escherichia coli Ribosomes which Interact Directly with Natural mRNA

Contact Info

Product

Resources

About