Dependence of Initiation Factor IF-2 Activity on Proteins L7 and L12 from Escherichia coli 50 S Ribosomes

Ribosomal protein L7/L12 is required for GTPase translation factors EF-G, RF3, and IF2 to bind in their GTP state to 70S ribosomes

Ribosomal protein L7/L12 is associated with translation initiation, elongation, and termination by the 70S ribosome. The guanosine 5' triphosphate hydrolase (GTPase) activity of elongation factor G (EF-G) requires the presence of L7/L12, which is critical for ribosomal translocation. Here, we have developed new methods for the complete depletion of L7/L12 from Escherichia coli 70S ribosomes to analyze the effect of L7/L12 on the activities of the GTPase factors EF-G, RF3, IF2, and LepA. Upon removal of L7/L12 from ribosomes, the GTPase activities of EF-G, RF3, and IF2 decreased to basal levels, while the activity of LepA decreased marginally. Upon reconstitution of ribosomes with recombinant L12, the GTPase activities of all GTPases returned to full activity. Moreover, ribosome binding assays indicated that EF-G, RF3, and IF2 require L7/L12 for stable binding in the GTP state, and LepA retained > 50% binding. Lastly, an EF-G∆G' truncation mutant possessed ribosome-dependent GTPase activity, which was insensitive to L7/L12. Our results indicate that L7/L12 is required for stable binding of ribosome-dependent GTPases that harbor direct interactions to the L7/L12 C-terminal domains, either through a G' domain (EF-G, RF3) or a unique N-terminal domain (IF2). Furthermore, we hypothesize this interaction is concomitant with counterclockwise ribosomal intersubunit rotation, which is required for translocation, initiation, and post-termination.

Phosphorylation of initiation factor eIF2 in response to stress conditions is mediated by acidic ribosomal P1/P2 proteins in Saccharomyces cerevisiae

Eukaryotic cells contain an unusually large cytoplasmic pool of P1/P2 phosphoproteins, which form the highly flexible 60S subunit stalk that is required to interact with and activate soluble translation factors. In cells, cytoplasmic P1/P2 proteins are exchanged for ribosome-bound proteins in a process that can modulate ribosome function and translation. Here, we analysed different S. cerevisiae stalk mutants grown under stress conditions that result in eIF2α phosphorylation. These mutants either lack a cytoplasmic pool of stalk proteins or contain free but not ribosome-bound proteins. Only cells that contain free P1/P2 proteins induce eIF2 phosphorylation in vivo in response to glucose starvation or osmotic stress. Moreover, we show that free S. cerevisiae P1/P2 proteins can induce in vitro phosphorylation of the initiation factor eIF2 by stimulating the autophosphorylation and activation of GCN2 kinase. Indeed, these ribosomal proteins do not stimulate other eIF2α kinases, such as PKR and HRI. P1/P2 and the known GCN2 activator deacylated tRNA compete for stimulating the eIF2α kinase activity of GCN2, although the P1/P2 proteins are considerably more active. These findings reveal a capacity of free cytoplasmic ribosomal stalk components to stimulate eIF2α phosphorylation, which in turn would modulate translation in response to specific forms of stress that may be linked with the previously described regulatory function of the ribosomal stalk.

Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNA(fMet) positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.

Asymmetric interactions between the acidic P1 and P2 proteins in the Saccharomyces cerevisiae ribosomal stalk

The Saccharomyces cerevisiae ribosomal stalk is made of five components, the 32-kDa P0 and four 12-kDa acidic proteins, P1alpha, P1beta, P2alpha, and P2beta. The P0 carboxyl-terminal domain is involved in the interaction with the acidic proteins and resembles their structure. Protein chimeras were constructed in which the last 112 amino acids of P0 were replaced by the sequence of each acidic protein, yielding four fusion proteins, P0-1alpha, P0-1beta, P0-2alpha, and P0-2beta. The chimeras were expressed in P0 conditional null mutant strains in which wild-type P0 is not present. In S. cerevisiae D4567, which is totally deprived of acidic proteins, the four fusion proteins can replace the wild-type P0 with little effect on cell growth. In other genetic backgrounds, the chimeras either reduce or increase cell growth because of their effect on the ribosomal stalk composition. An analysis of the stalk proteins showed that each P0 chimera is able to strongly interact with only one acidic protein. The following associations were found: P0-1alpha.P2beta, P0-1beta.P2alpha, P0-2alpha.P1beta, and P0-2beta.P1alpha. These results indicate that the four acidic proteins do not form dimers in the yeast ribosomal stalk but interact with each other forming two specific associations, P1alpha.P2beta and P1beta.P2alpha, which have different structural and functional roles.

Characterization of the domains of E. coli initiation factor IF2 responsible for recognition of the ribosome

We have studied the interactions between the ribosome and the domains of Escherichia coli translation initiation factor 2, using an in vitro ribosomal binding assay with wild-type forms, N- and C-terminal truncated forms of IF2 as well as isolated structural domains. A deletion mutant of the factor consisting of the two N-terminal domains of IF2, binds to both 30S and 50S ribosomal subunits as well as to 70S ribosomes. Furthermore, a truncated form of IF2, lacking the two N-terminal domains, binds to 30S ribosomal subunits in the presence of IF1. In addition, this N-terminal deletion mutant IF2 possess a low but significant affinity for the 70S ribosome which is increased by addition of IF1. The isolated C-terminal domain of IF2 has no intrinsic affinity for the ribosome nor does the deletion of this domain from IF2 affect the ribosomal binding capability of IF2. We conclude that the N-terminus of IF2 is required for optimal interaction of the factor with both 30S and 50S ribosomal subunits. A structural model for the interaction of IF2 with the ribosome is presented.

Structure-function relationships in the ribosomal protein L12 in the archaeon Sulfolobus acidocaldarius

A series of mutant L12 ribosomal proteins was prepared by site-directed mutations in the L12 protein gene of the archaeon Sulfolobus acidocaldarius. The mutant protein genes were overexpressed in Escherichia coli, and the products purified and incorporated into ribosomal cores which had been ethanol extracted to remove wild-type L12 protein. Measurements were made to determine if the mutation affected the binding of the L12 protein to the ribosome core or affected the translational activity of the resulting ribosome. Changing tyrosine [3] or tyrosine [5], conserved in all archaea and present in all eukarya in positions [3] and [7], to phenylalanine had no effect on binding or translational activity while changes to glycine significantly reduced binding and translational activity. Changing the single arginine [37] residue, conserved in almost all archaeal and eukaryal L12 proteins, to lysine, glutamic acid, glutamine, or glycine had no effect on binding to the core and had little or no significant effect on translational activity. The same was true when lysine [39], conserved in all archaeal L12 proteins, was changed to arginine, glutamic acid, glutamine, or glycine. Changing phenylalanine [104], the penultimate amino acid at the C-terminal end, which is conserved in all archaeal and eukaryal L12 proteins, to tyrosine or glycine had no effect on binding but lowered the translational activity by 60 and 75%, respectively, suggesting that this amino acid plays an important role in translation. Deletion of the highly charged region in the C-terminal domain, which is present in all archaeal and eukaryal L12 proteins, decreased transitional activity by 50%, suggesting this region is also involved in factor interactions.

The L7/L12 ribosomal domain of the ribosome: structural and functional studies

The L7/L12 protein forms a functionally important domain in the ribosome. This domain is involved in interaction with translation factors during protein biosynthesis. The tertiary and quaternary structure of the L7/L12 protein was established as a result of intensive studies in solution and in the ribosome. The conformational changes of L7/L12, the elongation factors Tu and G and other ribosomal proteins were traced by different experimental techniques. These changes occur upon interaction of the ribosome with the elongation factors and depend on GTP hydrolysis in accordance with the functional states of the ribosome.

An inhibitor of elongation factor G (EF-G) GTPase present in the ribosome wash of Escherichia coli: a complex of initiation factors IF1 and IF3?

An inhibitor of elongation factor G (EF-G) GTPase isolated from the ribosome wash of Escherichia coli was shown to stimulate the poly(A,U,G)- and initiation factor 2 (IF2)-dependent binding of N-formyl-[35S]Met-tRNAfMet to ribosomes. In the presence of saturating amounts of the EF-G GTPase inhibitor, neither addition of initiation factor 1 (IF1) nor addition of initiation factor 3 (IF3) caused a further stimulation of the formation of N-formyl-[35S]Met-tRNAfMET/poly(A,U,G)/ribosome complexes. Both IF1 and IF3 were shown to inhibit ribosome-dependent EF-G GTPase, especially when both initiation factors were added either in absence or in the presence of initiation factor 2 (IF2), poly(A,U,G) and N-formyl-Met-tRNAfMet. Therefore, we conclude that the EF-G GTPase inhibitor consisting of two polypeptide subunits with apparent molecular masses of 23,000 and 10,000 Da is a complex of initiation factors IF1 and IF3. The inhibition of EF-G GTPAse by IF3, but not the effects of IF1 in the presence or absence of IF3 could be reversed by increasing the Mg(2+)-concentration as already shown for the EF-G GTPase inhibitor. Therefore, IF1 as well as the EF-G GTPase inhibitor do not influence the ribosome-dependent EF-G GTPase by affecting the association of ribosomal subunits.

Properties and regulation of the GTPase activities of elongation factors Tu and G, and of initiation factor 2

During protein synthesis the interaction with ribosomes of elongation factors Tu (EF-Tu), G (EF-G) and initiation factor 2 (IF-2) is associated with the hydrolysis of GTP which is directly related to the functions of the factors. In this article we review systematically the properties of these GTPase activities in the presence and absence of protein synthesis, and by examining the characteristics of the different minimal systems for the expression of these activities we point to the role of the various effectors and to the enzymological aspects of the systems. For EF-Tu, it has been possible to eliminate any requirement for macromolecular effectors, showing that the factor itself is a GTPase. For EF-G, the presence of at least the 50S ribosomal subunit has remained a requirement, whereas IF-2 needs both the 50S and 30S subunits to exhibit GTPase activity. Between the GTPase activities of the three factors there are some striking similarities, but important differences prevail as a consequence of the specificity of the different functions. This can also be seen by examining the respective ribosomal regions implicated in these reactions. When coupled with protein synthesis, the three GTPase activities reveal characteristics differing from those observed in partial systems.

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.

Phosphorylation of acidic ribosomal proteins from rabbit reticulocytes by a ribosome-associated casein kinase

Two acidic proteins from 80-S ribosomes were isolated and purified to homogeneity. The purified acidic proteins could be phosphorylated by casein kinase using [gamma-32P]ATP and [gamma-32P]GTP as a phosphoryl donor. The proteins became phosphorylated in situ, too. Sodium dodecyl sulfate polyacrylamide gel analysis of the purified acidic proteins and 80-S particles showed identical phosphoproteins in the 16 000 dalton region.

Characterization and site of action of a soluble protein that stimulates peptide-bond synthesis

A recently identified soluble protein, named EF-P, stimulates peptide bond synthesis from ribosomal-bound N-formylmethionyl-tRNA and the aminoacyl-tRNA analog, puromycin. Using this model of peptide bond formation we have purified this activity approximately 100-fold from ribosome-free extracts of Escherichia coli. In order to study the mechanism by which the EF-P factor stimulates peptide bond formation, we examined and compared the requirements and site of action of the spontaneous and the EF-P-mediated synthesis of peptide bonds. We find that "enzymic" peptide bond synthesis (+EF-P) is characterized by relatively broad temperature and NH4Cl optima, a sharp Mg2+ optimum at 12 mM, and an apparent pKa of approximately 8.5. The characteristics of enzymic peptide bond synthesis closely resemble those reported for native peptidyl-puromycin formation rather than other models of peptide synthesis. Factor EF-P requires both 30-S and 50-S subunits for activity. The 30-S particle is inactive by itself and may function in the reaction merely to bind the fMet-tRNA substrate. Both the peptidyl transferase and the EF-P binding site may be part of the 50-S subunit. Unlike all other propagation factors, EF-P does not require the 50-S ribosomal proteins L7 and L12 and may therefore occupy a different ribosomal site.

The involvement of protein L11 in the joining of the 30-S initiation complex to the 50-S subunit

Ribosomal protein L11 participates in the coupling of the 30-S initiation complex with the 50-S subunit. P37 cores, lacking L7, L8, L12, L33, L10 and L11 were reconstituted with L7 and L10. These particles are unable to join successfully to the 30-S initiation complex, whereas reconstitution of the same cores in the presence of L7, L10 and L11 restores 60-80% of the original coupling activity. P0 cores lacking only L7, L8, L12 and L33 are able to carry out one round of initiation, addition of L7 resulting in complete restoration of full activity. The data obtained with these P37 core particles resemble those obtained with untreated 50-S particles carrying thiostrepton, which prevents the binding of initiation factor IF-2 into the 70-S initiation complex. It is postulated that L11 induces a niche on the ribosomal surface to facilitate the proper binding of the IF-2 X GTP X fMet-tRNA complex. This binding of IF-2 enables the 30-S initiation complex to join to the 50-S subunit, because of the associative ability of IF-2. If joining is impaired than both the level of fMet-tRNA binding and of the IF-2-mediated GTP hydrolysis is lowered.