Interaction of animal mitochondrial EF-Tu.EF-Ts with aminoacyl-tRNA, guanine nucleotides, and ribosomes

The mammalian mitochondrial complex consisting of elongation factors EF-Tu and EF-Ts (EF-Tu.Tsmt) is capable of efficiently binding aminoacyl-tRNA to the ribosome in the presence and absence of guanine nucleotides. In the presence of GTP the binding reaction is catalytic. In the absence of guanine nucleotides, or in the presence of a non-hydrolyzable GTP analog, only one round of ribosome binding occurs. EF-Tu.Tsmt is capable of forming a ternary complex with GTP and Escherichia coli Phe-tRNA as demonstrated by gel filtration chromatography, nitrocellulose filter binding, and by protection of the aminoacyl-tRNA bond from hydrolysis. GDP and the non-hydrolyzable GTP analog guanyl-5'-yl imidodiphosphate are also capable of facilitating ternary complex formation with EF-Tu.Tsmt, but are less effective. No kinetic advantage results from the formation of this ternary complex prior to ribosome binding, and EF-Tu.Tsmt may actually bind aminoacyl-tRNA directly to the ribosome prior to binding GTP. These results suggest that a variation of the prokaryotic elongation cycle is occurring in animal mitochondria. N-Ethylmaleimide inhibits the activity of EF-Tu.Tsmt in polymerization and in ribosome binding. However, the activity of the EF-Tsmt which can be measured independently, is not altered.     

Ef-Ts elongation factor interacts with elongation factor EF-Tu on ribosomes prior to the GTP hydrolysis stage

Methods of high-speed centrifugation and limited proteolysis were used to probe the interaction of EF-Tu with EF-Ts on the ribosome. It is shown that EF-Ts dissociates from EF-Tu only after EF-Tu-mediated GTP hydrolysis, i.e. EF-Ts within the EF-Tu.ribosome complexes in the pre-GTP-hydrolysis state co-sediments with the ribosomes and its rate of proteolysis is distinct from that of free EF-Ts. Moreover, as seen from the difference in sensitivity to trypsin of ribosomal proteins L19 and L27 EF-Ts affects the interaction of EF-Tu with the ribosome.     

GE2270A-resistant mutations in elongation factor Tu allow productive aminoacyl-tRNA binding to EF-Tu.GTP.GE2270A complexes

The antibiotic GE2270A prevents stable complex formation between elongation factor Tu (EF-Tu) and aminoacyl-tRNA (aatRNA). In Escherichia coli we characterized two mutant EF-Tu species with either G257S or G275A that lead to high GE2270A resistance in poly(Phe) synthesis, which at least partially explains the high resistance of EF-Tu1 from GE2270A producer Planobispora rosea to its own antibiotic. Both E. coli mutants were unexpectedly found to bind GE2270A nearly as well as wild-type (wt) EF-Tu in their GTP-bound conformations. Both G257S and G275A are in or near the binding site for the 3' end of aatRNA. The G257S mutation causes a 2.5-fold increase in affinity for aatRNA, whereas G275A causes a 40-fold decrease. In the presence of GE2270A, wt EF-Tu shows a drop in aatRNA affinity of at least four orders of magnitude. EF-Tu[G275S] and EF-Tu[G275A] curtail this drop to about two or one order, respectively. It thus appears that the resistance mutations do not prevent GE2270A from binding to EF-Tu.GTP and that the mutant EF-Tus may accommodate GE2270A and aatRNA simultaneously. Interestingly, in their GDP-bound conformations the mutant EF-Tus have much less affinity for GE2270A than wt EF-Tu. The latter is explained by a recent crystal structure of the EF-Tu.GDP.GE2270A complex, which predicts direct steric problems between GE2270A and the mutated G257S or G275A. These mutations may cause a dislocation of GE2270A in complex with GTP-bound EF-Tu, which then no longer prevents aatRNA binding as in the wt situation. Altogether, the data lead to the following novel resistance scenario. Upon arrival of the mutant EF-Tu.GTP.GE2270.aatRNA complex at the ribosomal A-site, the GTPase centre is triggered. The affinities of aatRNA and GE2270A for the GDP-bound EF-Tu are negligible; the former stays at the A-site for subsequent interaction with the peptidyltransferase centre and the latter two dissociate from the ribosome.     

Stabilization of the ternary complex EF-Tu.GTP.valyl-tRNA by ammonium salts

In a search for crystallizing conditions for the ternary complex EF-Tu.GTP.valyl-tRNA^val, the influence of various salts on its stability has been examined by measuring the rate of deacylation of the aminoacyl-tRNA in the complex. The most striking result is the general higher stability in solutions of ammonium salts and, in particular, the enhancement of this effect by sulphate and citrate. Thus sodium sulphate and citrate lead to destabilization of the complex, as expected from conventional considerations of adding salt, whereas the corresponding ammonium salts stabilize the complex as shown, for example, by an increase in the half-life of the valyl-tRNA^val in the complex from about 20 hours to at least 300 hours in the presence of 1.2 M ammonium sulphate. These results suggest that ammonium sulphate and ammonium citrate might be very suitable precipitants for crystallization studies of the ternary complex.     

The archaeal elongation factor 1alpha bound to GTP forms a ternary complex with eubacterial and eukaryal aminoacyl-tRNA.

The archaeal Sulfolobus solfataricus elongation factor 1alpha (SsEF-1alpha) bound to GTP or to its analogue guanyl-5'-yl imido diphosphate [Gpp(NH)p] formed a ternary complex with either Escherichia coli Val-tRNAVal or Saccharomyces cerevisiae Phe-tRNAPhe as demonstrated by gel-shift and gel-filtration experiments. Evidence of such an interaction also came from the observation that SsEF-1alphaz.rad;Gpp(NH)p was able to display a protective effect against either the spontaneous deacylation or the digestion of aminoacyl-tRNA by RNase A. Protection against the deacylation of aminoacyl-tRNA allowed evaluatation of the affinity of SsEF-1alphaz. rad;Gpp(NH)p for both aminoacyl-tRNAs used. The K'd values of the ternary complex containing S. cerevisiae Phe-tRNAPhe or E. coli Val-tRNAVal were 0.3 microM and 4.4 microM, respectively. In both cases, the affinity of SsEF-1alphaz.rad;Gpp(NH)p for aminoacyl-tRNA was three orders of magnitude lower than that of the homologous eubacterial ternary complexes, but comparable with the affinity shown by the ternary complex involving eukaryal EF-1alpha [Negrutskii, B.S. & El'skaya, A.V. (1998) Prog. Nucleic Acids Res. 60, 47-77]. As already observed with eukaryal EF-1alpha, SsEF-1alpha in its GDP-bound form was also able to protect the ester bond of aminoacyl-tRNA, even though with a 10-fold lower efficiency compared with SsEF-1alphaz.rad;Gpp(NH)p. The overall results indicated that the archaeal elongation factor 1alpha shares several properties with eukaryal EF-1alpha but not with eubacterial EF-Tu.     

Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodiumfalciparum plastid

Protein translation in the plastid (apicoplast) of Plasmodium spp. is of immense interest as a target for potential anti-malarial drugs. However, the molecular data on apicoplast translation needed for optimisation and development of novel inhibitors is lacking. We report characterisation of two key translation elongation factors in Plasmodium falciparum, apicoplast-encoded elongation factor PfEF-Tu and nuclear-encoded PfEF-Ts. Recombinant PfEF-Tu hydrolysed GTP and interacted with its presumed nuclear-encoded partner PfEF-Ts. The EF-Tu inhibitor kirromycin affected PfEF-Tu activity in vitro, indicating that apicoplast EF-Tu is indeed the target of this drug. The predicted PfEF-Ts leader sequence targeted GFP to the apicoplast, confirming that PfEF-Ts functions in this organelle. Recombinant PfEF-Ts mediated nucleotide exchange on PfEF-Tu and homology modeling of the PfEF-Tu:PfEF-Ts complex revealed PfEF-Ts-induced structural alterations that would expedite GDP release from PfEF-Tu. Our results establish functional interaction between two apicoplast translation factors encoded by genes residing in different cellular compartments and highlight the significance of their sequence/structural differences from bacterial elongation factors in relation to inhibitor activity. These data provide an experimental system to study the effects of novel inhibitors targeting PfEF-Tu and PfEF-Tu.PfEF-Ts interaction. Our finding that apicoplast EF-Tu possesses chaperone-related disulphide reductase activity also provides a rationale for retention of the tufA gene on the plastid genome.     

Evidence for activities of rabbit reticulocyte elongation factor 1 analogous to bacterial factors EF-Ts and EF-Tu

Preparations have been obtained from rabbit reticulocyte elongation factor 1 (EF-1) that exhibit activities analogous to the heat stable and heat labile factors, EF-Ts and EF-Tu, of $\text{Escherichia coli}$. The heat stable fraction, prepared by heating EF-1 in the presence of GTP, has virtually no activity in poly (U)-directed polyphenylalanine synthesis. The fraction exhibiting activity similar to bacterial EF-Tu is obtained by the interaction of EF-1 with GTP and phenylalanyl-tRNA followed by passage of the solution through a nitrocellulose filter. The filtrate, which alone has low activity in polyphenylalanine synthesis, when combined with the heat stable fraction gives high activity suggesting that the heat stable preparation catalyzes recycling of the filtrate component.     

Formation of the ternary complex EF-Tu.GTP.Phe-tRNA in the translation system ofStreptomyces aureofaciens

The efficiency of formation of the ternary complex consisting of the elongation factor Tu and Phe-tRNA’s fromEscherichia coli andStreptomyces aureofaciens was tested to explain the lower activity of thein vitro poly(U) translation system fromS. aureofaciens. Both factors were shown to be functionally interchangeable in the ternary complex formation with Phe-tRNA from eitherE. coli orS. aureofaciens. However, the efficiency of binding ofS. aureofaciens Phe-tRNA to EF-Tu was much lower with both factors.     

GTP interacts with the gamma-subunit of eukaryotic initiation factor eIF-2

Eukaryotic initiation factor eIF-2 is an oligomeric protein consisting of three different subunits. During initiation of protein synthesis eIF-2 interacts with GTP, Met-tRNAf and 40 S ribosomal subunit. By affinity labeling with a photo-reactive GTP analogue it was shown that in the binary complex [eIF-2 X GTP] GTP is in contact with the gamma-subunit of eIF-2.     

Reactivity of essential histidine residues in EF-Tu.GDP and EF-Tu.GTP from Escherichia coli

The microenvironment of histidine residues located in the binding site of elongation factor EF-Tu from Escherichia coli for the 3' terminus of aminoacyl-tRNA is altered during transition of EF-Tu.GDP to EF-Tu.GTP.     

Elongation factor (EF-Tu) gene probe detects polymorphism in Mycoplasma strains

Abstract Polymorphism in mycoplasma strains was observed by Southern blot hybridization of the digested mycoplasma DNAs with the elongation factor (EF-Tu) gene tuf of Escherichia coli . The hybridization patterns revealed genotypic heterogeneity among Mycoplasma gallisepticum strains and a remarkable degree of homogeneity among Mucoplasma pneumoniae strains isolated from pneumonia patients. The distinction among M. gallisepticum strain clusters achieved by the tuf gene probe corresponded exactly with that obtained with the rRNA gene probe pMC5. The tuf gene probe may thus be added as another effective tool in the taxonomy of Mollicutes and in epidemiological surveys of mycoplasma infections.     

Isolation,crystallisation, and preliminary X-ray analysis of the bovine mitochondrial EF-Tu:GDP and EF-Tu:EF-Ts complexes

Previous studies have shown that when bovine mitochondrial elongation factor Ts (EF-Ts) is expressed in Escherichia coli, it forms a tightly associated complex with E. coli elongation factor Tu (EF-Tu). In contrast to earlier experiments, purification of free mitochondrial EF-Ts was accomplished under nondenaturing conditions since only about 60% of the expressed EF-Ts copurified with E. coli EF-Tu. The bovine mitochondrial EF-Tu:GDP complex, the homologous mitochondrial EF-Tu:EF-Ts complex, and the heterologous E. coli/mitochondrial EF-Tu:EF-Ts complex were isolated and crystallised. The crystals of the EF-Tu:GDP complex diffract to 1.94 A and belong to space group P2(1) with cell parameters a=59.09 A, b=119.78 A, c=128.89 A and beta=96.978 degrees. The crystals of the homologous mitochondrial EF-Tu:EF-Ts complex diffract to 4 A and belong to space group C2 with cell parameters a=157.7 A, b=151.9 A, c=156.9 A, and beta=108.96 degrees.     

Co-purification of the aminoacyl-tRNA synthetase complex with the elongation factor eEF1

A multi-enzyme complex of mammalian aminoacyl-tRNA synthetases was isolated from rabbit reticulocytes, and purified by polyethylene glycol fractionation and gel filtration on Biogel A15m and affinity chromatography on tRNA-Sepharose. The synthetase complex contains nine synthetase activities, and the corresponding proteins as analyzed by SDS polyacrylamide gel electrophoresis. Three of the proteins showed the identical subunit molecular weights to those of the reticulocyte's elongation factor eEF1H. The eEF1 alpha protein could not be removed by second tRNA-Sepharose column chromatography, or gel filtration on Biogel A5m or Biogel A15m. Antibodies against eEF1 alpha react with the purified synthetase complex on the basis of dot blot analysis. This finding should provide new clues for elucidating the structural organization of the mammalian protein biosynthetic machinery.     

Analysis of rate constants governing the exchange of guanine nucleotides bound to EF-Tu catalysed by EF-Ts.

The kinetics of the heterologous exchange of GDP bound to EF-Tu by free GTP catalysed by EF-Ts have been analysed with a view to correlating results obtainable with different computational procedures. The affinity of EF-Ts for EF-Tu.GTP was found to be somewhat less than previously proposed by Romero et al. (Biochemistry 260, 6167:1985) though still greater than for EF-Tu.GDP. There is a close interrelationship between the constants for the binding of GTP to EF-Tu.EF-Ts and of EF-Ts to EF-Tu.GTP. The declining fractional rate of exchange observed by Romero et al. during displacement of GDP by GTP appears to be dependent on the ratio of the rate constants (k-1 + k-2)k4/k1k-2 as defined in the text, not on that of K4/K1 as they proposed.     

Predicting the binding affinities of misacylated tRNAs for Thermus thermophilus EF-Tu.GTP

The free energies for the binding of 20 different unmodified Escherichia coli elongator aminoacyl-tRNAs to Thermus thermophilus elongation factor Tu (EF-Tu) were determined. When combined with the binding free energies for the same tRNA bodies misacylated with either valine or phenylalanine determined previously [Asahara, H., and Uhlenbeck, O. C. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 3499-3504], these data permit the calculation of the contribution of each esterified amino acid to the total free energy of binding of the complex. The two data sets can also be used to calculate the free energy of binding of EF-Tu to any misacylated E. coli tRNA, and the values agree well with previously published experimental values. In addition, a survey of active misacylated suppressor tRNAs suggests that a minimal threshold of binding free energy for EF-Tu is required for suppression to occur.     

Determination of the kinetics of guanine nucleotide exchange on EF-Tu and EF-Ts: continuing uncertainties

An analysis is made of the rate constants for the reactions involving the interactions of EF-Tu, EF-Ts, GDP, and GTP recently derived by Gromadski et al. [Biochemistry 41 (2002) 162]. Though their measured values appear to allow a reasonable rate of nucleotide exchange sufficient to support rates of protein synthesis in vivo, their data underestimate the thermodynamic barrier involved in nucleotide exchange and therefore cannot be considered definitive. A kinetic scheme consistent with the thermodynamic barrier can be achieved by modification of various rate constants, particularly of those involving the release of EF-Ts from EF-Tu.GTP.EF-Ts, but such constants are markedly different from what are experimentally observed. It thus remains impossible at present satisfactorily to model guanine nucleotide exchange on EF-Tu, catalysed by EF-Ts by a double displacement mechanism, with experimentally derived rate constants. Metabolic control analysis has been applied to determine the degree of flux control of the different steps in the pathway.     

The complex formation between Escherichia coli aminoacyl-tRNA, elongation factor Tu and GTP. The effect of the side-chain of the amino acid linked to tRNA

The interaction between Escherichia coli aminoacyl-tRNAs and elongation factor Tu (EF-Tu) x GTP was examined. Ternary complex formation with Phe-tRNAPhe and Lys-tRNALys was compared to that with the respective misaminoacylated Tyr-tRNAPhe and Phe-tRNALys. There was no pronounced difference in the efficiency of aminoacyl-tRNA x EF-Tu x GTP complex formation between Phe-tRNAPhe and Tyr-tRNAPhe. However, Phe-tRNALys was bound preferentially to EF-Tu x GTP as compared to Lys-tRNALys. This was shown by the ability of EF-Tu x GTP to prevent the hydrolysis of the aminoacyl ester linkage of the aminoacyl-tRNA species. Furthermore, gel filtration of ternary complexes revealed that the complex formed with the misaminoacylated tRNALys was also more stable than the one formed with the correctly aminoacylated tRNALys. Both misaminoacylated aminoacyl-tRNA species could participate in the ribosomal peptide elongation reaction. Poly(U)-directed synthesis of poly(Tyr) using Tyr-tRNAPhe occurred to a comparable extent as the synthesis of poly(Phe) with Phe-tRNAPhe. In the translation of poly(A) using native Lys-tRNALys, poly(Lys) reached a lower level than poly(Phe) when Phe-tRNALys was used. It was concluded that the side-chain of the amino acid linked to a tRNA affects the efficiency of the aminoacyl-tRNA x EF-Tu x GTP ternary complex formation.     

Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome

GTP hydrolysis by elongation factor Tu (EF-Tu) on the ribosome is induced by codon recognition. The mechanism by which a signal is transmitted from the site of codon-anticodon interaction in the decoding center of the 30S ribosomal subunit to the site of EF-Tu binding on the 50S subunit is not known. Here we examine the role of the tRNA in this process. We have used two RNA fragments, one which contains the anticodon and D hairpin domains (ACD oligomer) derived from tRNA(Phe) and the second which comprises the acceptor stem and T hairpin domains derived from tRNA(Ala) (AST oligomer) that aminoacylates with alanine and forms a ternary complex with EF-Tu. GTP. While the ACD oligomer and the ternary complex containing the Ala-AST oligomer interact with the 30S and 50S A site, respectively, no rapid GTP hydrolysis was observed when both were bound simultaneously. The presence of paromomycin, an aminoglycoside antibiotic that binds to the decoding site and stabilizes codon-anticodon interaction in unfavorable coding situations, did not increase the rate of GTP hydrolysis. These results suggest that codon recognition as such is not sufficient for GTPase activation and that an intact tRNA molecule is required for transmitting the signal created by codon recognition to EF-Tu.