Binding interactions between radiolabeled Escherichia coli elongation factor G and the ribosome

Intramolecular movements in EF-G, trapped at different stages in its GTP hydrolytic cycle, probed by FRET

Elongation factor G (EF-G) is one of several GTP hydrolytic proteins (GTPases) that cycles repeatedly on and off the ribosome during protein synthesis in bacterial cells. In the functional cycle of EF-G, hydrolysis of guanosine 5'-triphosphate (GTP) is coupled to tRNA-mRNA translocation in ribosomes. GTP hydrolysis induces conformational rearrangements in two switch elements in the G domain of EF-G and other GTPases. These switch elements are thought to initiate the cascade of events that lead to translocation and EF-G cycling between ribosomes. To further define the coupling mechanism, we developed a new fluorescent approach that can detect intramolecular movements in EF-G. We attached a fluorescent probe to the switch I element (sw1) of Escherichia coli EF-G. We monitored the position of the sw1 probe, relative to another fluorescent probe anchored to the GTP substrate or product, by measuring the distance-dependent, Förster resonance energy transfer between the two probes. By analyzing EF-G trapped at five different functional states in its cycle, we could infer the cyclical movements of sw1 within EF-G. Our results provide evidence for conformational changes in sw1, which help to drive the unidirectional EF-G cycle during protein synthesis. More generally, our approach might also serve to define the conformational dynamics of other GTPases with their cellular receptors.

Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome

We have trapped elongation factor G (EF-G) from Escherichia coli in six, functionally defined states, representing intermediates in its unidirectional catalytic cycle, which couples GTP hydrolysis to tRNA-mRNA translocation in the ribosome. By probing EF-G with trypsin in each state, we identified a substantial conformational change involving its conserved switch I (sw1) element, which contacts the GTP substrate. By attaching FeBABE (a hydroxyl radical generating probe) to sw1, we could monitor sw1 movement (by approximately 20 A), relative to the 70S ribosome, during the EF-G cycle. In free EF-G, sw1 is disordered, particularly in GDP-bound and nucleotide-free states. On EF-G*GTP binding to the ribosome, sw1 becomes structured and tucked inside the ribosome, thereby locking GTP onto EF-G. After hydrolysis and translocation, sw1 flips out from the ribosome, greatly accelerating release of GDP and EF-G from the ribosome. Collectively, our results support a central role of sw1 in driving the EF-G cycle during protein synthesis.

Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation

Translocation is an essential step in the elongation cycle of the protein synthesis that allows for the continual incorporation of new amino acids to the growing polypeptide. Movement of mRNA and tRNAs within the ribosome is catalyzed by EF-G binding and GTP hydrolysis. The 30S subunit decoding center is crucial for the selection of the cognate tRNA. However, it is not clear whether the decoding center participates in translocation. We disrupted the interactions in the decoding center by mutating the universally conserved 16S rRNA bases G530, A1492, and A1493, and the effects of these mutations on translocation were studied. Our results show that point mutation of any of these 16S rRNA bases inhibits EF-G-dependent translocation. Furthermore, the mutant ribosomes showed increased puromycin reactivity in the pretranslocation complexes, indicating that the dynamic equilibrium of the peptidyl tRNA between the classical and hybrid-state configurations is influenced by contacts in the decoding center.

Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome

Following peptide bond formation, transfer RNAs (tRNAs) and messenger RNA (mRNA) are translocated through the ribosome, a process catalyzed by elongation factor EF-G. Here, we have used a combination of chemical footprinting, peptidyl transferase activity assays, and mRNA toeprinting to monitor the effects of EF-G on the positions of tRNA and mRNA relative to the A, P, and E sites of the ribosome in the presence of GTP, GDP, GDPNP, and fusidic acid. Chemical footprinting experiments show that binding of EF-G in the presence of the non-hydrolyzable GTP analog GDPNP or GDP.fusidic acid induces movement of a deacylated tRNA from the classical P/P state to the hybrid P/E state. Furthermore, stabilization of the hybrid P/E state by EF-G compromises P-site codon-anticodon interaction, causing frame-shifting. A deacylated tRNA bound to the P site and a peptidyl-tRNA in the A site are completely translocated to the E and P sites, respectively, in the presence of EF-G with GTP or GDPNP but not with EF-G.GDP. Unexpectedly, translocation with EF-G.GTP leads to dissociation of deacylated tRNA from the E site, while tRNA remains bound in the presence of EF-G.GDPNP, suggesting that dissociation of tRNA from the E site is promoted by GTP hydrolysis and/or EF-G release. Our results show that binding of EF-G in the presence of GDPNP or GDP.fusidic acid stabilizes the ribosomal intermediate hybrid state, but that complete translocation is supported only by EF-G.GTP or EF-G.GDPNP.

Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome

The region around position 1067 in domain II of 23S rRNA frequently is referred to as the GTPase center of the ribosome. The notion is based on the observation that the binding of the antibiotic thiostrepton to this region inhibited GTP hydrolysis by elongation factor G (EF-G) on the ribosome at the conditions of multiple turnover. In the present work, we have reanalyzed the mechanism of action of thiostrepton. Results obtained by biochemical and fast kinetic techniques show that thiostrepton binding to the ribosome does not interfere with factor binding or with single-round GTP hydrolysis. Rather, the antibiotic inhibits the function of EF-G in subsequent steps, including release of inorganic phosphate from EF-G after GTP hydrolysis, tRNA translocation, and the dissociation of the factor from the ribosome, thereby inhibiting the turnover reaction. Structurally, thiostrepton interferes with EF-G footprints in the alpha-sarcin stem loop (A2660, A2662) located in domain VI of 23S rRNA. The results indicate that thiostrepton inhibits a structural transition of the 1067 region of 23S rRNA that is important for functions of EF-G after GTP hydrolysis.

Ribosomes and ribosomal RNA as chaperones for folding of proteins

BACKGROUND

Provocative recent reports indicate that the large subunits of either prokaryotic or eukaryotic ribosomes have the capacity to promote refolding of denatured enzymes.

RESULTS

Salt-washed Escherichia coli ribosomes are shown to promote refolding of denatured rhodanese. The ability of the ribosomes to carry out renaturation is a property of the 50S ribosomal subunit, specifically the 23S rRNA. Refolding and release of enzymatically active rhodanese leaves the ribosomes in an inactive state or conformation for subsequent rounds refolding. Inactive ribosomes can be activated by elongation factor G (EF-G) plus GTP or by cleavage of their 23S rRNA by alpha-sarcin. Activation by either mechanism is strongly inhibited by the EF-G.GDP.fusidic acid complex.

CONCLUSIONS

Large subunits of E. coli ribosomes, specifically 23S rRNA, have the capacity to mediate refolding of denatured rhodanese. Refolding activity is related to the state or conformation of ribosomes that is promoted by EF-G. Activation by either mechanism is strongly inhibited by the EF-G.GDP.fusidic acid complex.

Nuclear magnetic resonance techniques for studying structure and function of ribosomes

The following conclusions can be drawn from the use of NMR techniques for studies of ribosomes: 1. The majority of ribosomal proteins are rigidly fixed within the particles, and the most mobile components in the isolated ribosome are L7/L12 proteins from the large subunit. 2. Interaction of EF-G with ribosomes results in some changes in ribosomal domains, and, particularly, immobilization of L7/L12 proteins takes place. The changes may pertain to the translocation reaction, since complexes with ribosomes, EF-G, and GTP are functional. The results of these studies using 1H NMR show that structural studies with this technique are limited as only a few proteins express their resonances in the 1H NMR spectra (S1, L7/L12). At the same time such studies are not exhaustive, since only the simplest samples were studied (ribosomes, the ribosomal complex with EF-G). Complexes with other ligands (tRNA, EF-Tu) have not yet been studied. It is also possible to enhance the resolution of 1H NMR techniques with the help of deuterated factors, ribosomes, and proteins, and to adapt the use of NMR to other nuclei (e.g., the use of fluorinated labels or incorporation of fluoroamino acids into the proteins). Many other approaches using NMR in biology have still to be explored. Therefore it is hoped that the use of NMR techniques will prove to be very useful in studies of the different functional steps of protein biosynthesis.

Pyrethroid inhibition of basal and calmodulin stimulated Ca2+ ATPase and adenylate cyclase in rat brain

Effects of two classes of pyrethroids, permethrin and resmethrin (type I), cypermethrin and deltamethrin (type II), on basal (calmodulin-deficient) and calmodulin stimulated activities of Ca2+ ATPase and adenylate cyclase from rat brain were studied in vitro. None of the pyrethroids inhibited synaptosomal basal Ca2+ ATPase, but permethrin and deltamethrin inhibited basal adenylate cyclase in the nuclear fraction of a brain homogenate. Both groups of pyrethroids decreased the calmodulin activated Ca2+ ATPase and adenylate cyclase from brain synaptosomes and nuclear fraction. The results indicate that calmodulin-stimulated Ca2+ ATPase is more sensitive to type II pyrethroids and pyrethroids are more effective on calmodulin stimulated enzymes than basal enzyme activities. Since calmodulin, adenylate cyclase and Ca2+ ATPase are known to participate in various brain processes, it is possible that pyrethroids alter neural transmission, however, additional in vivo work would be needed to confirm this possibility.

Mechanism of ribosomal translocation. Translocation limits the rate of Escherichia coli elongation factor G-promoted GTP hydrolysis

The pre-steady-state kinetics of GTP hydrolysis catalysed by elongation factor G and ribosomes from Escherichia coli has been investigated by the method of quenched-flow. The GTPase activities either uncoupled from or coupled to the ribosomal translocation process were characterized under various experimental conditions. A burst of GTP hydrolysis, with a kapp value greater than 30 s-1 (20 degrees C) was observed with poly(U)-programmed vacant ribosomes, either in the presence or absence of fusidic acid. The burst was followed by a slow GTP turnover reaction, which disappears in the presence of fusidic acid. E. coli tRNAPhe, but not N-acetylphenylalanyl-tRNAPhe (N-AcPhe-tRNAPhe), stimulates the GTPase when bound in the P site. If the A site of poly(U)-programmed ribosomes, carrying tRNAPhe in the P site, is occupied by N-AcPhe-tRNAPhe, the burst of Pi discharge is replaced by a slow GTP hydrolysis. Since, under these conditions, N-AcPhe-tRNAPhe is translocated from the A to the P site, this GTP hydrolysis very probably represents a GTPase coupled to the translocation reaction.

Synthetic and binding studies on the calcium binding site I of bovine brain calmodulin. II. Synthesis and CD studies on the cyclic 20-31 sequence

The synthesis of the cyclic 20-31 sequence of bovine brain calmodulin corresponding to the loop of the hypothetical calcium binding site I of the protein has been accomplished by classical solution methods. The interaction of the synthetic cyclic fragment with calcium ions has been investigated by CD spectroscopy in water and in 98% trifluoroethanol solution. Calcium ions have no effect on the dichroic absorption of aqueous solution of the cyclic dodecapeptide in the wavelength range 200-250 nm. In 98% trifluoroethanol the CD spectrum of the cyclic compound in the absence of calcium ions is almost identical to that of the linear dodecapeptide in the presence of saturation concentrations of calcium. This result supports our previous hypothesis of a folding of the linear sequence upon interaction with the metal ion. The cyclic peptide also interacts with calcium ions in 98% trifluoroethanol forming a 1:1 complex.

Ca2+-binding proteins: a comparative study of their behavior during high-performance liquid chromatography using gradient elution on reverse-phase supports

Reverse-phase high-performance liquid chromatography has been shown to be applicable to the isolation of Ca2+-binding proteins, specifically parvalbumins, from tissue extracts or from preparations first purified by "conventional" chromatography. Through an investigation of the behavior of a series of Ca2+-binding proteins as a function of buffer composition, pH, and organic eluant it has been possible to define mild conditions allowing for chromatography of the proteins in their native states. The elution positions of parvalbumins were not observed to correlate with the "overall" protein hydrophobicity, calculated using hydrophobicity values for the individual amino acids, thus indicating that factors such as hydrophobic/hydrophilic surface areas are important in determining the degree of association with the support. The usefulness of reverse-phase chromatography as an analytical tool for determining protein homogeneity is illustrated. Samples which had been isolated via "conventional" chromatography methods, and thought to be homogeneous, were observed to contain multiple species of the same protein.

Chemical cross-linking of elongation factor G to both subunits of the 70-S ribosomes from Escherichia coli

Ribosomal proteins situated at or near the binding site of elongation factor G (EF-G) on the Escherichia coli ribosome have been identified by use of the bifunctional, cleavable cross-linker, dimethyl-4,9-diaza-5,8-dioxo-6,7-dihydroxy-dodecanebisimidate. Five different bimolecular EF-G x ribosomal-protein complexes were isolated electrophoretically. The ribosomal proteins found in each of these complexes were identified as the 50-S-subunit proteins L6, L7/L12 and L14 and the 30-S-subunit proteins S12 and S19. In the presence of thiostrepton, which prevents binding of EF-G to the ribosome, there was a considerable decrease in the yield of each of these cross-linked complexes. The data suggest that EF-G is bound close to the ribosomal subunit interface.

Photochemical cross-linking of elongation factor G to 70-S ribosomes from Escherichia coli by 4-(6-formyl-3-azidophenoxy)butyrimidate

Ribosomal proteins situated at or near the binding site of elongation factor G (EF-G) on the Escherichia coli ribosome have been identified by use of the heterobifunctional cross-linker 4-(6-formyl-3-azidophenoxy)butyrimidate. Four different preparations of EF-G, in which the number of cross-linker molecules coupled to EF-G ranged from four to seven, all cross-linked to 50-S subunit proteins L1, L3 and L11 as well as to 30-S subunit proteins S3 and S4. Cross-linking of EF-G to ribosomal proteins was tested electrophoretically. In the case of L7/L12 and L11 immunological methods were also used. Cross-linking of EF-G to L1, L3, L11, S3 and S4 is specific as judged from the fact that addition of unmodified EF-G and of thiostrepton results in less cross-linking. The cross-linking data suggests that the binding site for EF-G includes several proteins which are located at the interface between the 30-S and 50-S subunits.

Escherichia coli elongation factor G blocks stringent factor

The relationship between the binding domains of elongation factor G(EF-G) and stringent factor (SF) on ribosomes was studied. The binding of highly purified, radioactively labeled, protein factors to ribosomes was monitored with a column system. The data show that binding of EF-G to ribosomes in the presence of fusidic acid and GDP or of the noncleavable analogue GDPCP prevents subsequent binding of SF to ribosomes. In addition, stabilization of the EF-G-ribosome complex by fusidic acid inhibits SF's enzymatic activities. Removal of protein L7/L12 from ribosomes leads to weaker binding of EF-G, while SF's binding and activity are unaffected. In the absence of L7/L12, EF-G-dependent inhibition of SF binding and function is reduced. The data presented in this report suggest that these two factors bind at overlapping, or at least interacting, ribosomal domains.

The mode of action of thiostrepton in the initiation of protein synthesis

The inhibition by thiostrepton of the initiation of protein synthesis is exerted at a different level from the inhibition of reactions mediated by EF-Tu and EF-G in the elongation of protein synthesis. The presence of thiostrepton on the 50-S subunit completely prevents the binding of the EF-Tu - GTP - aa-tRNA complex and EF-G - GTP complex to the 70-S ribosome, resulting in cessation of protein synthesis at a concentration of 1 muM thiostrepton. On the other hand, during initiation thiostrepton impairs the coupling of the 50-S subunit with the 30-S initiation complex, indirectly causing inhibition of IF-2-dependent reactions. Impairment of the coupling is strongly influenced by the conditions of incubation. Since formation of formylmethionylpuromycin and the IF-2-dependent GTP hydrolysis are inhibited to the same extent and recycling of IF-2 can take place in the presence of thiostrepton, we conclude that the basic mechanism of inhibition of initiation differs from that of inhibition of elongation.