Binding of protein synthesis initiation factor IF1 to 30 S ribosomal subunits: effects of other initiation factors and identification of proteins near the binding site.

The effects of other components of the initiation complex on Escherichia coli initiation factor IFI binding to 30 S ribosomal subunits were studied. Binding of [¹⁴C]IF1 in the absence of other initiation complex components was slight. Addition of either IF2 or IF3 stimulated binding to a variable extent. Maximum binding was observed when both IF2 and IF3 were present. Addition of GTP, fMet-tRNA, and phage R17 RNA caused little or no further stimulation of [¹⁴C]IF1 binding. A maximum of 0.5 molecule of [¹⁴C]IF1 bound per 30 S subunit in the presence of an excess of each of the three factors over 30 S subunits.Complexes of 30 S subunits, [¹⁴C]IF1, IF2, and IF3 were treated with the bifunctional protein cross-linking reagent dimethyl suberimidate in order to identify the ribosomal proteins near the binding site for IF1. Non-cross-linked [¹⁴C]IF1 was removed from the complexes by sedimentation through buffer containing a high salt concentration, and total protein was extracted from the pelleted particles. Approximately 12% of the [¹⁴C]IF1 was recovered in the pellet fraction. The mixture of cross-linked products was analyzed by polyacrylamide/sodium dodecyl sulfate gel electrophoresis. Autoradiography of the gel showed radioactive bands with molecular weights of 21,000, 25,000, and many greater than 120,000. The results indicate that [¹⁴C]IF1 was cross-linked directly to at least two ribosomal proteins. Analysis of the cross-linked mixture by radioimmunodiffusion with specific antisera prepared against each of the 30 S ribosomal proteins showed radioactivity in the precipitin bands formed with antisera against S12 and S19, and in lower yield with those against S1 and S13. Antiserum against IF2 also showed [¹⁴C]IF1 in the precipitin band. The results show that [¹⁴C]IF1 was present in covalently cross-linked complexes containing 30 S ribosomal proteins S1, S12, S13 and S19, and initiation factor IF2. The same ribosomal proteins have been implicated in the binding sites for IF2 and IF3. The results suggest that the three initiation factors bind to the 30 S subunit at the same or overlapping sites.     

Cross-linking of initiation factor IF3 to proteins of the Escherichia coli 30 S ribosomal subunit

Complexes of 30 S subunits and [¹⁴C]IF3 were allowed to react with the protein cross-linking reagents, N,N′-p-phenylenedimaleimide or dimethylsuberimidate. Non-cross-linked IF3 was removed from the complex by centrifugation in a buffer containing a high salt concentration, and the total protein was extracted from the pelleted particles. The mixture of cross-linked products was analyzed by radioimmunodiffusion with antisera prepared against all of the individual 30 S ribosomal proteins. Radioactivity was found in the precipitin bands formed with antisera against ribosomal proteins S1, S11, S12, S13, S19 and S21. The results show that IF3 was present in covalent cross-linked complexes containing those 30 S ribosomal proteins and imply that they comprise or are near the binding site for initiation factor IF3.     

Immunochemical analysis of molecular forms of protein synthesis initiation factors in crude cell lysates of Escherichia coli

Three initiation factors (IF1, IF2, and IF3) have been highly purified from Escherichia coli and extensively characterized, but little is known about the molecular forms of these proteins as they occur in vivo. We have analyzed molecular-weight and charge forms in crude cell lysates by polyacrylamide gel electrophoresis followed by immunoblotting with antibodies specific for the initiation factors. Freshly grown bacterial cells were lysed by sonication in buffer containing sodium dodecyl sulfate, and the lysate was fractionated by gel electrophoresis. Proteins from the gel were electrotransferred to a nitrocellulose sheet which was treated with a specific rabbit antiserum followed by radiolabeled Staphylococcus aureus protein A. Autoradiography showed only one major band each for IF1 and IF3, exactly corresponding to the isolated factors. For IF2, two molecular-weight forms were detected which were identical with purified IF2a and IF2b. No evidence for precursor forms was found. Two-dimensional gel analysis showed no charge heterogeneity for IF1, IF2a, and IF3, but multiple forms were seen for IF2b. Analysis of phosphoproteins from cells grown in radioactive phosphate medium ruled out the possibility that phosphorylation occurs on the initiation factors, elongation factors, or ribosomal proteins.     

Cistron Specific Translation Control Protein in <Emphasis Type="Italic">Escherichia coli</Emphasis>

GENE expression may be controlled during translation by ribosomal selection of mRNAs or even individual cistrons. Escherichia coli initiation factors associated with ribosomes affect the binding of ribosomes to mRNA^1,2; initiation factor IF3, for instance, influences the specificity of mRNA-ribosome interaction^3,4. IF3 activity has been separated into several fractions which show various specificities for different mRNA cistrons^4–9. An important problem is the possibility of intracellular changes in IF3 activity^10–12. From uninfected E. coli, we have now isolated a protein which changes the specificity of IF3 toward different mRNAs; we call this interference factor i. Pure factor i binds to IF3 and specifically affects the translation of T4 and MS2 RNA. Whereas the initiation of translation of the MS2 coat protein cistron is inhibited by factor i, the synthetase cistron—when available—is more rapidly initiated in the presence of factor i. The overall translation of T4 mRNA appears unchanged by factor i, but certain cistrons are stimulated at the expense of others. Interfering factors such as factor i could be important in controlling translation in E. coli.     

Polypeptide chain initiation in eukaryotes. IV. Purification and properties of supernatant initiation factor from Artemia salina embryos

The eukaryotic supernatant initiation factor, described in earlier publications from this laboratory, has been isolated and purified over 3000-fold, to about 70 to 80% purity, from extracts of embryos of the brine shrimp Artemia salina. The native protein appears to consist of two equal subunits, each weighing approximately 74,000 daltons. Like the bacterial initiation factor IF2, its prokaryotic counterpart, the Artemia factor promotes the AUG-dependent binding of fMet-tRNA, or the poly (U)-dependent binding of N-acetyl-Phe-tRNA, to the small ribosomal subunit. However, unlike IF2, the reaction is GTP-independent and the factor functions catalytically for one molecule may promote the binding of up to 12 molecules of fMet-tRNA to 40 s subunits at 0 °C.     

Initiation factor and ribosome levels are coordinately controlled in Escherichia coli growing at different rates

The levels of initiation factors and other translational components were compared in crude lysates of Escherichia coli grown at different rates. Cells were grown in media containing [35S]sulfate and different carbon sources, and harvested during mid-exponential phase after about 10 generations of balanced growth. Initiation factors (IF), elongation factors (EF), and a number of ribosomal proteins were identified unambiguously in gel patterns following two-dimensional polyacrylamide gel electrophoresis. The molar concentration of each protein was calculated from measurements of the radioactivity in excised gel spots and knowledge of the sulfur content of each protein. We found that the ribosomal proteins and elongation factors were present in equimolar amounts except for L7/L12 and EF-Tu which were 4-fold and 5-fold more abundant, respectively, and that the levels of each protein increased in proportion to growth rate. These results are similar to ones obtained previously by other methods, and serve to confirm the validity of our method. We found that the levels of IF2a and IF3 also were approximately proportional to growth rate. We also measured the levels of all three initiation factors using a radioimmune assay, showed that the factors are present in equimolar amounts, and confirmed that their abundance increased in parallel with ribosomes. We conclude that initiation factor levels are coordinately regulated with one another and with ribosome and elongation factor levels.     

Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors

The assembly of initiation complexes is studied in a protein synthesis initiation assay containing ribosomal subunits, globin [¹²⁵I]mRNA, [³H]Met-tRNA_f, seven purified initiation factors, ATP and GTP. By omitting single components from the initiation assay, specific roles of the initiation factors, ATP and GTP are demonstrated. The initiation factor eIF-2 is required for the binding of Met-tRNA_f to the 40 S ribosomal subunit. The initial Met-tRNA_f binding to the small ribosomal subunit is a stringent prerequisite for the subsequent mRNA binding. The initiation factors eIF-3, eIF-4A, eIF-4B and eIF-4C together with ATP promote the binding of mRNA to the 40 S initiation complex. The association of the 40 S initiation complex with the 60 S ribosome subunit to form an 80 S initiation complex is mediated by the initiation factor eIF-5 and requires the hydrolysis of GTP. The factor eIF-1 gives a twofold overall stimulation of initiation complex formation. A model of the sequential steps in the assembly of the 80 S initiation complex in mammalian protein synthesis is presented.     

Archaeal translation initiation factor aIF2 can substitute for eukaryotic eIF2 in ribosomal scanning during mammalian 48S complex formation

Heterotrimeric translation initiation factor (IF) a/eIF2 (archaeal/eukaryotic IF 2) is present in both Eukarya and Archaea. Despite strong structural similarity between a/eIF2 orthologs from the two domains of life, their functional relationship is obscure. Here, we show that aIF2 from Sulfolobus solfataricus can substitute for its mammalian counterpart in the reconstitution of eukaryotic 48S initiation complexes from purified components. aIF2 is able to correctly place the initiator Met-tRNA_i into the P-site of the 40S ribosomal subunit and accompany the entire set of eukaryotic translation IFs in the process of cap-dependent scanning and AUG codon selection. However, it seems to be unable to participate in the following step of ribosomal subunit joining. In accordance with this, aIF2 inhibits rather than stimulates protein synthesis in mammalian cell-free system. The ability of recombinant aIF2 protein to direct ribosomal scanning suggests that some archaeal mRNAs may utilize this mechanism during translation initiation.     

A single mutation in the IF3 N-terminal domain perturbs the fidelity of translation initiation at three levels

Bacterial translation initiation factor 3 (IF3) is involved in the fidelity of translation initiation at several levels, including start-codon discrimination, mRNA translation, and initiator-tRNA selection. The IF3 C-terminal domain (CTD) is required for binding to the 30S ribosomal subunit. N-terminal domain (NTD) function is less certain, but likely contributes to initiation fidelity. Point mutations in either domain can decrease initiation fidelity, but C-terminal domain mutations may be indirect. Here, the Y75N substitution mutation in the NTD is examined in vitro and in vivo. IF3_Y75N protein binds 30S subunits normally, but is defective in start-codon discrimination, inhibition of initiation on leaderless mRNA, and initiator-tRNA selection, thereby establishing a direct role for the IF3 NTD in these initiation processes. A model illustrating how IF3 modulates an inherent function of the 30S subunit is discussed.     

Metabolic fate of initiation factors after inhibition of protein synthesis in Escherichia coli

Summary The metabolic fate of translation initiation factor after inhibition of protein synthesis by different means has been investigated. We have found a decay in initiation factor activity when protein synthesis is blocked by chloramphenicol but not during arginine starvation of PA1 (Rel^–) or PA2 (Rel⁺) strains or during puromycin incubation. These results suggest that inactivation of certain initiation factors occurs when the regeneration of ribosomal subunits from polysomes is inhibited in the cells.Complementation experiments indicate that IF₃ factor activity is preferentially affected during chloramphenicol treatment.Same preferential inhibition of IF₃ activity seems to occur during in vitro incubation of crude IF. 70S ribosomes or 30S subunits protect this factor against the inactivation. Preliminary results seem tosuggest that ATP is implicated in this in vitro inactivation process.     

Direct cross-links between initiation factors 1, 2, and 3 and ribosomal proteins promoted by 2-iminothiolane

Complexes were prepared containing 30S ribosomal subunits from Escherichia coli and the three initiation factors IF1, IF2, and IF3. In different experiments, each of the factors was radiolabeled with the others unlabeled. The complexes were allowed to react with 2-iminothiolane and then oxidized to promote the formation of intermolecular disulfide bonds, some of which were between factors and ribosomal proteins. Each of the labeled factors becomes covalently cross-linked to the complex as judged by its failure to dissociate when centrifuged in a sucrose gradient containing a high salt concentration. Proteins from the complexes were extracted and analyzed on two-dimensional polyacrylamide gels by nonequilibrium isoelectric focusing and sodium dodecyl sulfate gel electrophoresis. Spots corresponding to cross-linked dimers that contained initiation factors, as indicated on autoradiographs, were cut out and analyzed further. The following cross-linked dimers between factors and ribosomal proteins were identified: IF1-S12, IF1-S18, IF2-S13, IF3-S7, IF3-S11, IF3-S13, and IF3-S19. Cross-links between factors IF1-IF2 and IF3-IF2 were also identified. A model integrating these findings with others on the protein topography of the ribosome is presented.     

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA

The 970 loop (helix 31) of Escherichia coli 16S ribosomal RNA contains two modified nucleotides, m²G966 and m⁵C967. Positions A964, A969, and C970 are conserved among the Bacteria, Archaea, and Eukarya. The nucleotides present at positions 965, 966, 967, 968, and 971, however, are only conserved and unique within each domain. All organisms contain a modified nucleoside at position 966, but the type of the modification is domain specific. Biochemical and structure studies have placed this loop near the P site and have shown it to be involved in the decoding process and in binding the antibiotic tetracycline. To identify the functional components of this ribosomal RNA hairpin, the eight nucleotides of the 970 loop of helix 31 were subjected to saturation mutagenesis and 107 unique functional mutants were isolated and analyzed. Nonrandom nucleotide distributions were observed at each mutated position among the functional isolates. Nucleotide identity at positions 966 and 969 significantly affects ribosome function. Ribosomes with single mutations of m²G966 or m⁵C967 produce more protein in vivo than do wild-type ribosomes. Overexpression of initiation factor 3 specifically restored wild-type levels of protein synthesis to the 966 and 967 mutants, suggesting that modification of these residues is important for initiation factor 3 binding and for the proper initiation of protein synthesis.     

Purification and characterization of protein synthesis initiation factors IF1, IF2, and IF3 from Escherichia coli.

A simple procedure is described for the purification in high yields of protein synthesis initiation factors IF1, IF2, and IF3 from Escherichia coli strain MRE 600. IF2 was separated from IF1 and IF3 by ammonium sulfate fractionation and was purified by column chromatography on phosphocellulose and diethylaminoethyl (DEAE) Sephadex. IF1 and IF3 were separated by phosphocellulose column chromatography. IF1 was purified by molecular sieve chromatography, and IF3 by phosphocellulose column chromatography in urea buffer. Each factor was analyzed by sodium dodecyl sulfate or urea polyacrylamide gel electrophoresis and was greater than 98% pure. Only one form of IF1 and IF3 was found, with molecular weights of 8,500 and 22,500, respectively. Two forms of IF2 were isolated: IF2a with a molecular weight of 118,000 and IF2b with a molecular weight of 90,000. The amino acid composition of each factor was determined, and their stimulation in a variety of assays for initiation of protein synthesis is reported.     

Shutoff on Neuroblastoma Cell Protein Synthesis by Semliki Forest Virus: Loss of Ability of Crude Initiation Factors to Recognize Early Semliki Forest Virus and Host mRNA's

A crude ribosomal wash containing the initiation factors of protein synthesis was isolated from mouse neuroblastoma cells 8 h after infection with Semliki Forest virus (SFV). The activity of this wash was compared with that of a wash from control cells in a cell-free protein-synthesizing “pH5” system, with early SFV mRNA (42S), late SFV mRNA (26S), encephalomyocarditis virus (EMC) mRNA, or neuroblastoma polyadenylated mRNA templates. A pronounced loss of activity (±80%) of the crude ribosomal wash from infected cells was observed with host mRNA (neuroblastoma polyadenylated mRNA) and early SFV mRNA, messengers which contain a cap structure at the 5′ terminus. However, these washes were only slightly less active in systems programmed with (noncapped) EMC mRNA and late SFV mRNA. Although late SFV mRNA (26S) is capped, the synthesis of late (= structural) proteins in infected lysates was insensitive to inhibition by cap analogs. Purified initiation factors eIF-4B (M_r, 80,000) and cap-binding protein (M_r, 24,000) from reticulocytes (but none of the others) were able to restore the activity of infected factors to about 90% of control levels in systems programmed with early SFV mRNA and host mRNA. These observations indicate that infection-exposed crude initiation factors have a decreased level of eIF-4B and cap-binding protein activity. However, after partial purification of these and other initiation factors from infected and control cells, we found no significant difference in activity when model assay systems were used. Furthermore, both eIF-4B and cap-binding protein from infected cells were able to restore the activity of these infection-exposed factors to the same level obtained when these factors isolated from control cells or reticulocytes were added. A possible mechanism for the shutoff of host cell protein synthesis is discussed.     

The ribosome‐bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex

Bacterial translation initiation factor 2 (IF2) is a GTPase that promotes the binding of the initiator fMet‐tRNA^fMet to the 30S ribosomal subunit. It is often assumed that IF2 delivers fMet‐tRNA^fMet to the ribosome in a ternary complex, IF2·GTP·fMet‐tRNA^fMet. By using rapid kinetic techniques, we show here that binding of IF2·GTP to the 30S ribosomal subunit precedes and is independent of fMet‐tRNA^fMet binding. The ternary complex formed in solution by IF2·GTP and fMet‐tRNA is unstable and dissociates before IF2·GTP and, subsequently, fMet‐tRNA^fMet bind to the 30S subunit. Ribosome‐bound IF2 might accelerate the recruitment of fMet‐tRNA^fMet to the 30S initiation complex by providing anchoring interactions or inducing a favourable ribosome conformation. The mechanism of action of IF2 seems to be different from that of tRNA carriers such as EF‐Tu, SelB and eukaryotic initiation factor 2 (eIF2), instead resembling that of eIF5B, the eukaryotic subunit association factor.     

Thermodynamics of GTP and GDP Binding to Bacterial Initiation Factor 2 Suggests Two Types of Structural Transitions

During initiation of messenger RNA translation in bacteria, the GTPase initiation factor (IF) 2 plays major roles in the assembly of the preinitiation 30S complex and its docking to the 50S ribosomal subunit leading to the 70S initiation complex, ready to form the first peptide bond in a nascent protein. Rapid and accurate initiation of bacterial protein synthesis is driven by conformational changes in IF2, induced by GDP-GTP exchange and GTP hydrolysis. We have used isothermal titration calorimetry and linear extrapolation to characterize the thermodynamics of the binding of GDP and GTP to free IF2 in the temperature interval 4-37 °C. IF2 binds with about 20-fold and 2-fold higher affinity for GDP than for GTP at 4 and 37 °C, respectively. The binding of IF2 to both GTP and GDP is characterized by a large heat capacity change (− 868 ± 25 and − 577 ± 23 cal mol^− 1 K^− 1, respectively), associated with compensatory changes in binding entropy and enthalpy. From our data, we propose that GTP binding to IF2 leads to protection of hydrophobic amino acid residues from solvent by the locking of switch I and switch II loops to the γ-phosphate of GTP, as in the case of elongation factor G. From the large heat capacity change (also upon GDP binding) not seen in the case of elongation factor G, we propose the existence of yet another type of conformational change in IF2, which is induced by GDP and GTP alike. Also, this transition is likely to protect hydrophobic groups from solvent, and its functional relevance is discussed.     

A model for the interaction of the G3‐subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit

Bacterial translation initiation factor IF2 complexed with GTP binds to the 30S ribosomal subunit, promotes ribosomal binding of fMet‐tRNA, and favors the joining of the small and large ribosomal subunits yielding a 70S initiation complex ready to enter the translation elongation phase. Within the IF2 molecule subdomain G3, which is believed to play an important role in the IF2‐30S interaction, is positioned between the GTP‐binding G2 and the fMet‐tRNA binding C‐terminal subdomains. In this study the solution structure of subdomain G3 of Geobacillus stearothermophilus IF2 has been elucidated. G3 forms a core structure consisting of two β‐sheets with each four anti‐parallel strands, followed by a C‐terminal α‐helix. In line with its role as linker between G3 and subdomain C1, this helix has no well‐defined orientation but is endowed with a dynamic nature. The structure of the G3 core is that of a typical OB‐fold module, similar to that of the corresponding subdomain of Thermus thermophilus IF2, and to that of other known RNA‐binding modules such as IF2‐C2, IF1 and subdomains II of elongation factors EF‐Tu and EF‐G. Structural comparisons have resulted in a model that describes the interaction between IF2‐G3 and the 30S ribosomal subunit.     

Temperature sensitivity of protein synthesis initiation in reticulocyte cell-free systems. A ribosomal factor which protects protein synthesis inactivation at elevated temperatures.

Inactivation of protein synthesis in the reticulocyte lysate system, which occurs when the system is incubated at 42 °C, was prevented by a high concentration KCl extract of the ribosomes. The KCl extract also supported protein synthesis at 42 °C by KCl-washed ribosomes. Three factor fractions (IF.15, IF.2, and IF.25) were separated from the extract and characterized in partial reactions of initiation. The factor IF.2 could prevent the inactivation of the factor IF.15-promoted protein synthesis by the washed ribosomes at 42 °C. IF.2 also overcame the decrease in IF.15-promoted 40S subunit-Met-tRNA_f complex at 42 °C. The protective activity of IF.2 was inactivated by N-ethylmaleimide. The activities of IF.15 and IF.2 were little affected by heating the factors at 42 °C. However, prewarming of KCl-washed ribosomes at 42 °C caused decreased protein synthesis in subsequent incubation at 34 °C with unwarmed factors. These results suggest that some components other than the initiation factors may be inactivated at 42 °C, which is prevented by IF.2 in the course of protein synthesis.