Studies on the binding of bacterial elongation factors EF Tu and EF G to ribosomes

When EF G² from Escherichia coli or Pseudomonas fluorescens is pre-bound to ribosomes in the presence of GMD, or GTP and fusidic acid, a differential effect is observed on the subsequent EF Tu-catalyzed binding of aminoacyl-tRNA to ribosomes. The EF G from E. coli nearly completely prevents the binding reaction, whereas the corresponding factor from P. fluorescens displays a significantly lower inhibitory effect. Both EF G factors form stable complexes with ribosomes and are equally efficient in the polymerization reaction. The difference in inhibitory properties between the two factors persists over a wide range of NH₄Cl concentration.     

Interaction of diphtheria toxin fragment A and of elongation factor 2 with Cibacron blue

Diphtheria toxin fragment A interacts with Cibacron blue in solution, although it is not retained by blue Sepharose columns. Difference spectral titration of fragment A with the dye gives a dissociation constant of the order of 10^–5 M and a 11 stoichiometry for the complex. In equilibrium dialysis experiments Cibacron blue behaves as a competitive inhibitor of the binding of NAD to diphtheria toxin fragment A. The dye inhibits in a non-competitive way the fragment A-catalysed transfer of ADP-ribose from NAD to elongation factor 2 (EF2). By affinity chromatography on blue Sepharose a binding of EF2 and of ADP-ribosyl-EF2 with the dye is also demonstrated. GDP, GTP and GDP(CH₂)P are able to displace EF2 from blue Sepharose.     

Studies on elongation factor II from calf brain

Elongation factor II (EF2) has been purified from calf brain, and its reactions with guanosine nucleotides and ribosomes have been studied. Its behavior is, in general, similar to that observed with EF2 from other eukaryote sources. Thus, in the presence of GTP or GDP, EF2 interacts with ribosomes to form a ribosome-EF2-GDP complex. Fusidic acid has little effect on the stability of this complex, which suggests that it is more stable than the corresponding complex from prokaryote systems. As assayed by a nitrocellulose filter technique, only GTP, GDP, dGTP and GDPCP are bound to ribosomes dependent on EF2. In the absence of ribosomes, an EF2-GTP or EF2-GDP complex can be detected. Fusidic acid at relatively high concentrations inhibits their formation, but diphtheria toxin in the presence of NAD does not. The EF2-GTP complex has been separated from unbound GTP by gel filtration, and the reactivity of the complex with ribosomes has been investigated. When EF2-GTP is incubated with ribosomes, GTP hydrolysis occurs, and evidence for a ribosome-EF2-GDP complex has been obtained. The results thus suggest that the EF2-GTP complex may be an intermediate in the binding of EF2 to ribosomes. Based on molecular sieve chromatography, it appears that the stability of these complexes is ribosome-EF2-GDP > EF2-GTP > EF2-GDP.     

Available sulphydryl groups of mammalian ribosomes in different functional states

The numbers of sulphydryl groups on NH₄Cl-washed rat liver polyribosomes in different functional states were measured under carefully standardized conditions with ¹⁴C-labelled N-ethylmaleimide and ³⁵S-labelled 5,5-dithio-bis(2-nitrobenzoic acid). Ribosomes denatured with urea had 120 titratable sulphydryl groups, 60 on each subunit, whereas native ribosomes invariably showed fewer available sulphydryl groups. Ribosomes stripped of transfer RNA (S-type ribosomes) had 55 available sulphydryl groups. Ribosomes bearing the growing peptidyl-tRNA at the acceptor site had 41 sulphydryl groups available. If these A-type ribosomes were labelled with ¹⁴C-labelled N-ethylmaleimide and dissociated into subunits, 23 of the labelled sulphydryl groups were found on the 60 S subunit and 19 on the 40 S subunit. After translocation of the peptidyl-tRNA to the donor position on ribosomes (D ribosomes), the number of available sulphydryl groups increased to 72, of which 43 were on the 60 S subunit and 29 on the 40 S subunit. This demonstrates that both subunits participate in the change of peptidyl-tRNA from the A to D positions. When the D ribosomes were reacted with EF2 (elongation factor) and GTP, the available sulphydryl groups increased to 82; addition of EF2 alone or with GDP, GDPCP or ATP failed to cause this increase, which has accordingly been attributed to an energy-dependent conformational change in the ribosome.Ribosomes were reconstructed from subunits with poly(U) and Phe-tRNA. In the presence of poly(U) only, a ribosome with 55 available SH groups was formed, thus corresponding to the stripped ribosomes. When both poly(U) and Phe-tRNA were present, a ribosome was formed with 44 available sulphydryl groups, corresponding approximately to an A-type ribosome. Since no EF1 or GTP was used in reconstructing this ribosome, these data indicate that the conformation of A-type ribosomes is not dependent on EF1 or GTP, but is due to the presence of tRNA at the acceptor site.We therefore incline to the view that the observed changes in available SH groups reflect conformational changes, with an opening up of ribosome structure as it progresses from having the peptidyl-tRNA at the A position to the D position and then binds EF2 and GTP, followed by a restoration of the more compact from when the incoming aminoacyl-tRNA is then bound.     

Function of bacteriophage Qbeta replicase containing an altered subunit IV

In order to elucidate the function of elongation factor Ts in Qβ replicase, enzyme was obtained from a Qβ-infected Escherichia coli mutant HAK88, which carries an altered EFTs² with a thermolabile catalytic activity. HAK88 Qβ replicase was found to be quite unstable at 42 °C. Further studies indicated that the mutant enzyme exhibits temperature sensitivity with regard to GTP binding ability but not with Qβ RNA and poly(C) binding. These results suggest that the function of EFTs in Qβ replicase is closely related to the binding of GTP to the enzyme.A defect in Qβ replicase also appears when it is reconstituted from the Qβ replicase subunit complex I–II and the HAK88 EFTu-EFTs complex. Several lines of evidence obtained by using the reconstituted enzyme suggest strongly that the EFTs function is involved specifically in initiation of RNA synthesis, but not in the elongation reaction.     

Requirements for the initiation of polyphenylalanine synthesis by recombined ribosomal subunits from yeast

A reaction stimulated by elongation factor 2 (EF-2) is necessary for the formation of the initial peptide-bond in poly(U)-directed peptide synthesis on yeast ribosomal subunits. The stimulation is inhibited by fusidic acid or diphtheria toxin together with NAD. It is assumed that the reaction of EF-2 represents translocation: in the presence of EF-2 almost twice the amount of N-acetyl-phenylalanyl-tRNA is bound to ribosomes and moreover, upon addition of puromycin a considerable stimulation of N-acetyl-phenylalanyl-puromycin formation is found. Contradictory data in the literature on this subject may be due to nonenzymatic translocation caused by a high monovalent cation concentration in the ribosome preparations or to an unspecific method for the extraction of N-acetyl-phenylalanyl-puromycin.     

The effect of removal or replacement with proflavine of the Y base in the anticodon loop of yeast tRNAPhe on binding into the acceptor or donor sites of reticulocyte ribosomes

Phe-tRNA from yeast has a highly modified nucleoside, called Y, adjacent to the 3′ side of its anticodon, that can be removed or replaced with proflavine. In a protein-synthesizing system from rabbit reticulocytes, poly (U)-directed binding and polyphenylalanine synthesis are low with these modified Phe-tRNA species relative to the corresponding values with unmodified Phe-tRNA. However, polymerization can be increased with relatively large amounts of elongation factor I. The modified Phe-tRNA species bound to the ribosomes with poly(U) either in the presence or absence of elongation factor I and GTP is immediately reactive in the peptidyl transferase reaction measured by the formation of diphenylalanine or phenylalanyl-puromycin. It appears to have been bound directly into the donor ribosomal site by either the nonenzymatic mechanism involving Mg²⁺ or by the enzymatic mechanism involving EF-I and GTP.     

Activation of sulphate in Anabaena cylindrica

Summary Crude cell-free extracts of Anabaena cylindrica synthesized adenosine-5-phosphosulphate (AP³⁵S) and 3-phosphoadenosine-5-phosphosulphate (PAP³⁵S) from ³⁵SO₄ ^2- in the presence of Mg²⁺, ATP and inorganic pyrophosphatase. Maximum AP³⁵S and PAP³⁵S were produced at pH 7.15 and 8.05, respectively. APS kinase was detected in the supernatant of crude cell-free extracts by a spectrophotometric procedure. ATP-Sulphurylase had an absolute requirement for Mg²⁺ and less than 30% AP³⁵S was formed when Mg²⁺ was replaced by either Mn²⁺ or Co²⁺. Nucleotide triphosphates other than ATP and 2-deoxyATP were ineffective in this reaction. Maximum enzyme activity was observed at equimolar concentrations of Mg²⁺ and ATP and excess of either of these was inhibitory. Other nucleotide triphosphates, like GTP, UTP, CTP, TTP, ITP, or 2-deoxyATP also inhibited the enzyme activity. Inhibition by GTP was competitive with respect to ATP. ATP-sulphurylase activity was not affected by cysteine, methionine or glutathione.Abbreviations APS adenosine-5-phosphosulphate - PAPS 3-phosphoadenosine-5-phosphosulphate     

Factor-free (“Non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes

Systems of poly(U)-directed polyphenylalanino synthesis by Escherichia coli ribosomes in the absence of elongation factors and GTP (factor-free system) or in the presence of one of the elongation factors and GTP (EF-G² and EF-T_u-deperident systems) are described. It is shown that the use of oligouridylates of different length as templates in the factor-free system results in peptides, the degree of polymerization of which does not exceed the number of template codons, i.e. a conjugated translocation of the peptidyl-tRNA and the template takes place. Thus, the function of translocation as well as the specific binding of aminoacyl-tRNA and transpeptidation proved to be intrinsic to the ribosome itself. The study of kinetics of polyphenylalanine synthesis and dependence of the synthesis rate on the Mg²⁺ concentration in the factor-free, EF-T_u-dependent and EF-G-dependent translation systems has demonstrated that the elongation factors with GTP promote ribosomal mechanisms of aminoacyl-tRNA binding and translocation, respectively. It turned out that the factor-free translation system does not display miscoding. It is the promotion of translocation by EF-G with GTP that has been found to be responsible in full measure for miscoding, while EF-T_U with GTP does not contribute to this.     

Isolation and Characterization of Collagen - Synthesizing Polysomes from Chick Embryos

Collagen - synthesizing polysomes were isolated by low-speed oentrifugation of the post-mitochomirial supernatant of chick homogenates. Electron microscopy of the fraction thus isolated shows it to be exclusively composed of ribosomes. Amino acid incorporation in vitro showed that these particles were efficient in the incorporation of proline, but not tryptophan, as opposed to ribosomes obtained from the supernatant of the low-speed oentrifugation. The incorporation process was highly dependent on GTP, and exibited an optimal Mg²⁺ concentration of 5.6 mN. The reaction was inhibited by RNase, elongation inhibitors as anysomycin, sparsomycin, fusidic acid and GDPCP. It was also moderately inhibited by initiation inhibitors such as aurintricarboxilic acid and pyrocatechol violet. The product of the incorporation was characterized as collagen by its sensitivity towards purified collagenase, lack of tryptophan, chromatography in CN-cellulose and molecular sieve chromatography in Sephadex G-200.     

Inhibition by ricin of protein synthesis in vitro. Ribosomes as the target of the toxin

1. Ricin (a toxic protein from the seeds of Ricinus communis) is a powerful inhibitor of the poly(U)-directed incorporation of phenylalanine into polypeptides catalysed by isolated rat liver ribosomes and elongation factors 1 and 2 (EF 1 and EF 2). The inhibition can be largely overcome by increasing the concentration of ribosomes. 2. The toxin does not affect the binding of phenylalanyl-tRNA to ribosomes catalysed by EF 1, nor does it inhibit the puromycin reaction used as a test for peptide-bond formation catalysed by ribosomes. 3. Ricin inhibits the ribosome-linked GTP hydrolysis catalysed by EF 2. 4. Ribosomes treated with ricin and washed through sucrose gradients containing 0.6m-NH(4)Cl are functionally inactive in those assay systems that are sensitive to the presence of added toxin. 5. It is suggested that ricin brings about an irreversible modification of ribosomes which impairs their ability to interact with EF 2. Since ricin inhibits at a molar concentration much lower than that of ribosomes it probably acts catalytically. No added cofactor is necessary for the inhibitory action of the toxin.     

Elongation factor Tu can reduce translation errors in poly(U)-directed cell-free systems

Rates of incorporation of [³H]phenylalanine and [¹⁴C]leucine from the aminoacylated transfer-RNA into polypeptides synthesized on poly(U) programmed Escherichia coli ribosomes have been determined in cell-free translation systems containing either elongation factors Tu and G with GTP, or just elongation factor Tu or G with GTP, or none of the elongation factors. The presence of elongation factor Tu with GTP has been shown to reduce the leucine to phenylalanine ratio in the product at relatively low concentrations of Mg²⁺. This error-reducing effect of elongation factor Tu has not been observed at high concentrations of Mg²⁺, although the factor still contributed to the speed of elongation. The results are discussed in terms of the kinetic proof-reading mechanism proposed by Hopfield (1974).     

Discrimination between aminoacyl groups on su+ 7 tRNA by elongation factor Tu

The su⁺7 nonsense suppressor of Escherichia coli is a mutant tRNA^Trp that can be aminoacylated with either tryptophan or glutamine. We have compared the ternary complexes of glutaminyl and tryptophanyl-su⁺7 tRNA with elongation factor Tu and GTP. Glutaminyl-su⁺7 tRNA binds more strongly than tryptophanyl-su⁺7 tRNA to EF Tu · GTP. The greatest distinction between the two species of the tRNA is seen in their dissociation rates from the complex, which differ by as much as fivefold. The distinction is affected by pH values around neutrality. These results show that EF Tu can distinguish between two aminoacyl-tRNAs which differ only in the aminoacyl group. The implications for the unusual amino acid specificity of su⁺7 tRNA are discussed.     

Inhibition by Thiopeptin of Bacterial Protein Synthesis

Thiopeptin, a sulfur-containing antibiotic, was found to inhibit protein synthesis in a bacterial ribosomal system. The pretreatment of ribosomal subunits with the antibiotic revealed that thiopeptin may act on the 50 S ribosomal subunit. The elongation of peptide chain on the ribosome is more profoundly blocked by the antibiotic than the initiation of protein synthesis. It was demonstrated that thiopeptin inhibits elongation factor (EF)-Tu-dependent GTP hydrolysis and binding of aminoacyl-tRNA to the ribosome. The peptidyl transferase-catalyzed puromycin reaction is not significantly affected by the antibiotic. Thiopeptin inhibits EF-G-associated GTPase reaction, and translocation of peptidyl-tRNA and mRNA from the acceptor site to the donor site. Protein synthesis in ribosomal systems, obtained from rat liver and rabbit reticulocytes are insensitive to the antibiotic.     

Aluminium impacts elements of the phosphoinositide signalling pathway in neuroblastoma cells

Inositol phosphate formation was examined in aluminium-treated murine neuroblastoma cells labelled with [³H]-myoinositol. Employing fluoride-stimulated intact cells, aluminium (0.2M to 1 mM) reduced inositol phosphate formation in a dose-dependent manner. In digitonin-permeabilized cells, stimulated with nonhydrolyzable GTP[S], inositol phosphate formation was also inhibited by increasing aluminium doses; the IC₅₀ value was about 20M aluminium, while the inositol phosphate level was reduced 2.5 to 3 fold by 50M aluminium. The inhibitory effect of aluminium (50M) could not be reversed by increasing GTP[S] concentrations up to 500M. Prechelation of aluminium to citrate or EGTA completely abolished the aluminium-triggered inhibition of fluoride-stimulated inositol phosphate formation in intact cells, but had little effect on the inhibition of permeabilized cells stimulated with GTP[S]. In neuroblastoma cells phosphoinositide hydrolysis could be evoked either through a pathway involving the Mg²⁺/guanine nucleotide binding (G_p) protein, or via a pathway operative in the presence of high intracellular Ca²⁺ concentrations. In the Mg²⁺/G_p protein-mediated pathway, formation of inositol triphosphate, IP₃, inositol diphosphate, IP₂, and inositol monophosphate, IP, was apparently inhibited by aluminium in an interdependent manner. As to the Ca²⁺-mediated pathway, aluminium application mainly diminished the release of IP₃. Following interiorization, aluminium thus acts upon elements critical for phosphoinositide-associated signal transduction. An aluminium target apparently resides on the G_p protein. Phosphatidylinositol-4,5-diphosphate-specific phospholipase C probably harbours a second aluminium target.     

Reduced puromycin sensitivity of translocated polysomes after the addition of elongation factor 2 and non-hydrolysable GTP analogues.

Treatment of reticulocyte polysomes with elongation factor eEF-2 and GTP led to an increased sensitivity of peptidyl-tRNA for puromycin as a result of the translocation from the ribosomal A-site to the P-site. Upon addition of an excess of the non-hydrolysable GTP analogue, GuoPP[CH2]P, the puromycin sensitivity decreased rapidly. The decrease in sensitivity required high concentrations of eEF-2 with half maximal effect at an eEF-2 concentration of around 1 microM. The data suggest either that peptidyl-tRNA had re-translocated back to the A-site due to the higher affinity of eEF-2 for the pre-translocation than for the post-translocation ribosome, or that the eEF-2-GuoPP[CH2]P complex blocks the peptidyl-transferase activity.     

The peptidyl-puromycin reaction with Neurospora crassa ribosomes

Summary The reaction of the peptidyl-tRNA in an in vitro system from Neurospora crassa with puromycin has been studied by different experimental approaches. Ribosomes precharged with labelled polyphenylalanine have been prepared and the release of radioactivity, occurring after the reaction with puromycin, has been followed on sucrose density gradients. Furthermore the reaction of endogenous peptidyl-tRNA carried by ribosomes isolated from actively growing mycelia with ³H-puromycin has been characterized. By this latter technique it has been possible to evaluate the percentage of ribosomes engaged in protein synthesis in ribosomal populations isolated from mycelia in different stages of growth.Abbreviations used TF-1 aminoacyl transferase I - TF-2 aminoacyl transferase II - PM puromycin - ³H-PM puromycin-methoxy-³H dihydrochloride - HEPES N-2-Hydroxyethylpiperazine-N-2-ethanesulfonic acid - TCA trichloroacetic acid - PEP phosphoenolpyruvate - tRNA transfer RNA - rRNA ribosomal RNA - PPO 2,5-diphenyloxazole - POPOP 1,4-bis-(5-phenyloxazol-2-yl) benzene     

Effect of elongation factor 2 and of adenosine diphosphate-ribosylated elongation factor 2 on translocation.

1. The effect of elongation factor 2 (EF 2) and of adenosine diphosphate-ribosylated elongation factor 2 (ADP-ribosyl-EF 2) on the shift of endogenous peptidyl-tRNA from the A to the P site of rat liver ribosomes (measured by the peptidyl-puromycin reaction) and on the release of deacylated tRNA (measured by aminoacylation) was investigated. 2. Limiting amounts of EF2, pre-bound or added to ribosomes, catalyse the shift of peptidyl-tRNA in the presence of GPT; when the enzyme is added in substrate amounts GMP-P(CH2)P [guanosine (beta, gamma-methylene)triphosphate] can partially replace GTP. ADP-ribosyl-EF 2 has no effect on the shift of peptidyl-tRNA when present in catalytic amounts, but becomes almost as effective as EF 2 when added in substrate amounts together with GTP; GMP-P(CH2)P cannot replace GTP. 3. The release of deacylated tRNA is induced only by substrate amounts of added EF 2 and also occurs in the absence of guanine nucleotides. In this reaction ADP-ribosyl-EF 2 is only 25% as effective as EF 2 in the absence of added nucleotide, but becomes 60-80% as effective in the presence of GTP or GMP-P(CH2)P. 4.The results obtained on protein-synthesizing systems are consistent with the hypothesis that ADP-ribosyl-EF 2 can operate a single round of translocation followed by binding of aminoacyl-tRNA and peptide-bond formation. 5. From the data obtained with the native enzyme it is concluded that the two moments of translocation require different conditions of interaction of EF 2 with ribosomes; it is suggested that the shift of peptidyl-tRNA is catalysed by EF 2 pre-bound to ribosomes, and that the release of tRNA is induced by a second molecule of interacting EF 2. The hydrolysis of GTP would be required for the release of pre-bound EF 2 from ribosomes. 5. The inhibition of the utilization of limiting amounts of EF 2 on ADP-ribosylation is very likely the consequence of a concomitant decrease in the rate of association and dissociation of the enzyme from ribosomes.