Studies on the ribosomal sites involved in factors Tu and G-dependent reactions

Elongation factor Ts directly facilitates the formation and disassembly of the Escherichia coli elongation factor Tu·GTP·aminoacyl-tRNA ternary complex

BACKGROUND

Aminoacyl-tRNA (aa-tRNA) enters the ribosome in a ternary complex with the G-protein elongation factor Tu (EF-Tu) and GTP.

RESULTS

EF-Tu·GTP·aa-tRNA ternary complex formation and decay rates are accelerated in the presence of the nucleotide exchange factor elongation factor Ts (EF-Ts).

CONCLUSION

EF-Ts directly facilitates the formation and disassociation of ternary complex.

SIGNIFICANCE

This system demonstrates a novel function of EF-Ts. Aminoacyl-tRNA enters the translating ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here, we describe bulk steady state and pre-steady state fluorescence methods that enabled us to quantitatively explore the kinetic features of Escherichia coli ternary complex formation and decay. The data obtained suggest that both processes are controlled by a nucleotide-dependent, rate-determining conformational change in EF-Tu. Unexpectedly, we found that this conformational change is accelerated by elongation factor Ts (EF-Ts), the guanosine nucleotide exchange factor for EF-Tu. Notably, EF-Ts attenuates the affinity of EF-Tu for GTP and destabilizes ternary complex in the presence of non-hydrolyzable GTP analogs. These results suggest that EF-Ts serves an unanticipated role in the cell of actively regulating the abundance and stability of ternary complex in a manner that contributes to rapid and faithful protein synthesis.

The structure and dynamics of ribosomal protein L12

The protein L12 in bacterial ribosomes is essential for the proper function of a number of factors involved in protein synthesis. The protein is mostly described in terms of a rigid structure despite the repeated observation of high flexibility. This paper gives a review of the structure and flexibility of L12 in relation to its function.

Studies on the modification of Escherichia coli ribosomal protein L7/L12 by succinic anhydride

Lysine modification by increasing quantities of succinic anhydride in the Escherichia coli ribosomal protein L7/L12 produces loss of its ability in reconstitution of elongation-factor-G-dependent GTP hydrolysis and polyphenylalanine synthesis activities, showing lower antigenicity and loss of antigenic determinants.

Chemistry and biology of E. coli ribosomal protein L12

E. coli ribosomal protein L12, because of its unique features, has been studied in more detail than perhaps any of the other ribosomal proteins. Unlike the other ribosomal proteins that are generally present in stoichiometric amounts, there are four copies of L12 per ribosome, some of which are acetylated on the N-terminal serine. The acetylated species, referred to as L7, has not been shown, as yet, to possess any different biological activity than L12. A specific enzyme that acetylates L12 to form L7, using acetyl-CoA as the acetyl donor, has been purified from E. coli extracts. L12 is also unique in that it does not contain cysteine, tryptophan, histidine, or tyrosine, is very acidic (pI: 4.85) and has a high content of ordered secondary structure (approximately 50%). The protein is normally found in solution as a dimer and also forms a tight complex with ribosomal protein L10. There are three methionine residues in L12, located in the N-terminal region of the protein, one or more of which are essential for biological activity. Oxidation of the methionines to methionine sulfoxide prevents dimer formation and inactivates the protein. The four copies of L12 are located in the crest region(s) of the 50S ribosomal subunit. There is good evidence that the soluble factors, such as IF-2, EF-Tu, EF-G and RF, interact with L12 on the ribosome during the process of protein synthesis. This interaction is essential for the proper functioning of each of the factors and for GTP hydrolysis associated with the individual partial reactions of protein synthesis. The L12 gene is located on an operon that contains the genes for L10 and beta beta' subunits of RNA polymerase at about 88 min on the bacterial chromosome. DNA-directed in vitro systems have been used to study the unique regulation of the expression of these genes. Autogenous regulation, translational control, and transcription attenuation are regulatory mechanisms that function to control the synthesis of these proteins.

Ribosomal protein L7/L12 is required for optimal translation

We have tested the performance in vitro of Escherichia coli ribosomes containing or lacking the protein L7/L12. When the experiments are performed in an optimized mixture of ions (polymix), L7/L12 is required for maximal rate of synthesis as well as for minimal missense error frequency. The results in conventional Tris/Mg2+/NH4Cl buffers are different; in these buffers, only the rate of synthesis is strongly dependent on the presence of L7/L12. In addition, we show that there is a large difference between the optimal Mg2+ concentration required for speed of translation and that for accuracy of translation in conventional buffer. These optima are very close in polymix. Finally, we show that the contribution of L7/L12 to the speed of translation is obscured in translation systems that are limited by substrates. We conclude that it is not possible to analyze details of the mechanism of translation in conventional buffers.

Hydrolysis of GTP on elongation factor Tu.ribosome complexes promoted by 2'(3')-O-L-phenylalanyladenosine

In the presence of Escherichia coli ribosomes and elongation factor EF) Tu, 2'(3')-O-L-phenylalanyladenosine (AdoPhe), the 3'-terminal portion of Phe-tRNAPhe, promotes the hydrolysis of GTP. The reaction requires the presence of both 30S and 50S ribosomal subunits and of proteins L7/L12 on the 50S subunit, is unaffected by mRNA [poly(uridylic acid)], and is strongly stimulated by EF-Ts. It is proposed that the AdoPhe-dependent GTP hydrolysis, like that promoted by aminoacyl-tRNA, is mediated by a ternary complex with EF-Tu and GTP; however, in contrast to aminoacyl-tRNA, AdoPhe is probably not retained by ribosomes after GTP hydrolysis. Phe-tRNAPhe or N-acetyl-Phe-tRNAPhe bound to the ribosomal acceptor site do not inhibit, but even stimulate, GTP hydrolysis by AdoPhe.EF-Tu.GTP. Thus, the binding site for EF-Tu on the ribosome is probably available for interaction with AdoPhe.EF-Tu.GTP regardless of whether the nearby acceptor site is vacant of occupied with aminoacyl-tRNA or peptidyl-tRNA. The results demonstrate the critical role of the 3'-terminal region of aminoacyl-tRNA in activating the EF-Tu- plus ribosome-dependent GTPase.

Dimer state of protein L7/L12 and EF-G-dependent reactions of ribosomes

A number of different monomer and dimer derivatives of protein L7/L12 has been studied in EF-G-dependent reactions on the ribosome. It has been shown that only dimer derivatives of protein L7/L12 are able to interact with the ribosome. This means that it is the dimer forms of protein L7/L12 that are present in the functionally active ribosome. It is likely that the N-terminal sequence of protein L7/L12 is responsible for dimerization of the protein in solution and at the same time contributes mainly to the interaction of the protein L7/L12 dimer with the ribosome. The results obtained suggest that there are four copies of protein L7/L12 in the translating ribosome.

Binding of thiostrepton to ribosomes from thiostrepton-sensitive and -resistant Bacillus subtilis strains

Binding of [(35)S]thiostrepton to ribosomes from thiostrepton-sensitive and -resistant strains of Bacillus subtilis was studied. Ribosomes from thiostrepton-resistant strains bound relatively little thiostrepton compared with ribosomes from thiostrepton-sensitive B. subtilis. In addition, ribosomes from revertant strains that were obtained as thiostrepton-sensitive revertants from thiostrepton-resistant strains bound [(35)S]thiostrepton similarly to ribosomes from the sensitive parental strain.

Thiostrepton-resistant mutants of Bacillus subtilis: localization of resistance to the 50S subunit

A number of thiostrepton-resistant mutants of Bacillus subtilis were obtained. The thi mutations map proximally to strA. Effects of thiostrepton on polyphenylalanine synthesis with ribosomes of S-100 fractions from parent and mutant strains indicated that resistance was localized to the ribosomes. Furthermore, effects of thiostrepton on binding of [3H]GTP to ribosomes and 50S subunits from thiostrepton-sensitive and -resistant strains localized the site of resistance to the 50S subunit. In addition, revertants from thiostrepton-resistance to thiostrepton-sensitivity were obtained. Ribosomes and 50S subunits from these thiostrepton-sensitive revertants were sensitive to thiostrepton similar to parental sensitive B. subtilis.

Thiostrepton inhibition of initiation factor 1 activity in polypeptide chain initiation in Escherichia coli

Thiostrepton, a peptide antibiotic, inhibits the GTP-dependent 70S initiation complex formation (as measured by binding of fMet-tRNA to ribosomes and concomitant hydrolysis of GTP) only when initiation factor 1 is present to permit catalytic recycling of initiation factor 2 in the initiation reaction. When initiation factor 1 is absent, the binding of fMet-tRNA and GTP hydrolysis occur stoichiometrically with respect to initiation factor 2, and thiostrepton has no effect on either reaction under these conditions. Detailed analysis of this inhibition process shows that thiostrepton prevents catalytic recycling of initiation factor 2 by blocking the action of initiation factor 1, which is required for the dissociation of initiation factor 2 from the 70S initiation complex. This dissociation is necessary for the catalytic reutilization of initiation factor 2 in the initiation reaction. The antibiotic does not directly inhibit GTP hydrolysis per se in initiation. The inhibition of fMet-tRNA binding to ribosomes by thiostrepton is also dependent on the concentration of GTP; the inhibition is most pronounced at low concentrations of GTP, but at a high molar ratio of GTP to thiostrepton, the inhibition is completely abolished.

Influence of cholesteryl 14-methylhexadecanoate on some ribosomal functions required for peptide elongation

1. Polyribosomes and ribosomal subunits from rat liver were adsorbed on a cellulosic ion-exchange adsorbent, freeze-dried and extracted with organic solvents. The activity of extracted particles in peptide elongation was tested in the presence of purified peptideelongation factors. 2. Chloroform-methanol mixture (2:1, v/v) extracted 1.87+/-0.15 pmol of cholesteryl 14-methylhexadecanoate/pmol of the smaller ribosomal subunit and 0.92+/-0.11 pmol/pmol of the larger subunit. 3. In the presence of transferase I, extracted polyribosomes and 40S subunits bound more phenylalanyl-tRNA than did control non-extracted particles. The same binding as in control mixtures was obtained with extracted particles supplemented with cholesteryl 14-methylhexadecanoate in quantities corresponding to those extracted. 4. The polymerization of phenylalanine was greatly decreased with extracted polyribosomes and subunits and addition of the cholesteryl ester could not fully restore the original activity. 5. Extraction significantly decreased the activity of the P site of peptidyl transferase and normal activity was recovered after the addition of the ester. The A site of peptidyl transferase in extracted polyribosomes showed an increased activity when compared with non-extracted polyribosomes. 6. Cholesteryl 14-methylhexadecanoate apparently affects the function of the ribosomal A site and peptidyl transferase site and probably also that of the guanosine triphosphatase site and P site. The presence of different amounts of the ester in polyribosomes may be one of the mechanisms modulating peptide elongation at the ribosomal level.

The requirement for ribosomal proteins L7 and L12 in peptide-chain termination

Proteins L7 and L12 from 50S ribosomal subunits of Escherichia coli are required for peptidechain termination. This termination process is inhibited by thiostrepton. Since both thiostrepton-treated ribosomes and those depleted of L7 and L12 have a markedly reduced ability to form release factor.UA[(3)H]A.ribosome complexes, the binding of release factors to the ribosome appears to be the primary site of inhibition.

Influence of guanine nucleotides and elongation factors on interaction of release factors with the ribosome

Release of formylmethionine from the reticulocyte ribosomal substrate, f[(3)H]Met-tRNA.ribosome, is promoted by reticulocyte release factor (RF). The initial rate of this reaction is stimulated by GTP but inhibited by GDPCP. Formation of an RF.UA[(3)H]A(2).ribosome complex is a measure of the binding of reticulocyte RF to the ribosome, and the recovery of this complex is increased by GDPCP and, to a lesser extent, GTP. These studies suggest that GTP is involved in the initial association of RF with the ribosome and that hydrolysis of the gamma-phosphate of the guanine nucleotide is required at a subsequent rate-limiting step. The ribosomal-dependent fMet-tRNA hydrolysis and GTPase activities of reticulocyte RF are inhibited when elongation factor (EF)-2 is bound to the respective ribosomal substrate in the presence of fusidic acid and GDP. When EF-G is bound to the f[(3)H]Met-tRNA.AUG.ribosome substrate with fusidic acid and GDP, the fMet-tRNA hydrolysis activity of Escherichia coli RF-1 and RF-2 is also inhibited. The binding of reticulocyte RF and E. coli RF-1 or RF-2 to their respective ribosomes is prevented when fusidic acid.EF-2/EF-G.GDP.ribosome complexes are used.

Assembly of bacterial ribosomes

I have not mentioned the remarkable progress made mainly by Fellner and his co-workers (86) in the elucidation of the primary structure of rRNA's and by Wittmann and his co-workers (87) in determining the structure of several ribosomal proteins. Such knowledge of primary structures is certainly the basis of complete understanding of the structure of the ribosome. With the current progress in technology, complete elucidation of the primary structure of all the ribosomal components is probably a matter of time. As indicated in this article, a rough approximation of the three-dimensional structure of ribosomes is likely to emerge soon. Although not mentioned in this article, studies of ribosomes from higher organisms are also progressing. We must, therefore, consider what further studies should be conducted and what kinds of questions we would like to solve. Some groups of investigators aim to elucidate the complete three-dimensional structure of ribosomes and to find out how these complex cell organelles function; they hope to determine the conformational changes of many of the component molecules within the ribosome structure in response to external macromolecules and cofactors engaged in protein synthesis. Such knowledge will also be important in enabling us to understand the regulation of translation of genetic messages. Other groups of investigators aim to elucidate the complex series of events which originate in the transcription of the more than 60 genes and culminate in the formation of the specific structure of the organelle. Complete reproduction in vitro of all the assembly events that occur in vivo should not be difficult to achieve in principle. It should then become possible to study in vitro any factor regulating the biogenesis of the organelle. Although we do not know whether such studies would reveal any new fundamental principle that governs the complex circuits of interconnected macromolecular interactions, the achievement of such a complete in vitro system would represent a necessary step in the comprehensive understanding of biogenesis of organelles, and eventually, of the more complex behavior and genesis of cells (89).