Further studies with labelled polypeptide-chain-initiation factor 3 (IF-3)

Structure-function analysis of Escherichia coli translation initiation factor IF3: tyrosine 107 and lysine 110 are required for ribosome binding

Translation initiation factor IF3 is required for peptide chain initiation in Escherichia coli. IF3 binds directly to 30S ribosomal subunits ensuring a constant supply of free 30S subunits for initiation complex formation, participates in the kinetic selection of the correct initiator region of mRNA, and destabilizes initiation complexes containing noninitiator tRNAs. The roles that tyrosine 107 and lysine 110 play in IF3 function were examined by site-directed mutagenesis. Tyrosine 107 was changed to either phenylalanine (Y107F) or leucine (Y107L), and lysine 110 was converted to either arginine (K110R) or leucine (K110L). These single amino acid changes resulted in a reduced affinity of IF3 for 30S subunits. Association equilibrium constants (M-1) for 30S subunit binding were as follows: wild-type, 7.8 x 10(7); Y107F, 4.1 x 10(7); Y107L, 1 x 10(7); K110R, 5.1 x 10(6); K110L, < 1 x 10(2). The mutant IF3s were similarly impaired in their abilities to specifically select initiation complexes containing tRNA(fMet). Toeprint analysis indicated that 5-fold more Y107L or K110R protein was required for proper initiator tRNA selection. K110L protein was unable to mediate this selection even at concentrations up to 10-fold higher than wild type. The results indicate that tyrosine 107 and lysine 110 are critical components of the ribosome binding domain of IF3 and, furthermore, that dissociation of complexes containing noninitiator tRNAs requires prior binding of IF3 to the ribosomes.

Interaction of bovine mitochondrial ribosomes with Escherichia coli initiation factor 3 (IF3)

Mammalian mitochondrial ribosomes are distinguished from their bacterial and eukaryotic-cytoplasmic counterparts, as well as from mitochondrial ribosomes of lower eukaryotes, by their physical and chemical properties and their high protein content. However, they do share more functional homologies with bacterial ribosomes than with cytoplasmic ribosomes. To search for possible homologies between mammalian mitochondrial ribosomes and bacterial ribosomes at the level of initiation factor binding sites, we studied the interaction of Escherichia coli initiation factor 3 (IF3) with bovine mitochondrial ribosomes. Bacterial IF3 was found to bind to the small subunit of bovine mitochondrial ribosomes with an affinity of the same order of magnitude as that for bacterial ribosomes, suggesting that most of the functional groups contributing to the IF3 binding site in bacterial ribosomes are conserved in mitochondrial ribosomes. Increasing ionic strength affects binding to both ribosomes similarly and suggests a large electrostatic contribution to the reaction. Furthermore, bacterial IF3 inhibits the Mg2+-dependent association of mitochondrial ribosomal subunits, suggesting that the bacterial IF3 binds to mitochondrial small subunits in a functional way.

Photochemical cross-linking of translation initiation factor 3 to Escherichia coli 50S ribosomal subunits

Translation initiation factor 3 (IF-3) was bound noncovalently to Escherichia coli 50S ribosomal subunits. Irradiation of such complexes with near-ultraviolet light (greater than 285 nm) resulted in covalent attachment of initiation factor 3 to the 50S subunit. Photo-cross-linking attained its maximum level of 40% of that which was noncovalently bound after 90 min of irradiation. Cross-linking was abolished in the presence of either 0.5 M NH4C1 or 0.25 mM aurintricarboxylic acid, indicating that specific binding of initiation factor 3 to the ribosome was a prerequisite for subsequent covalent attachment. Further analysis showed that all the IF-3 was covalently bound to a small number of 50S subunit proteins. The major cross-linked proteins were identified as L2, L7/L12, L11, and L27 by immunochemical techniques. These results are discussed in light of the proposed mechanism for IF-3 function.

Chain initiation factor 3 crosslinks to E. coli 30S and 50S ribosomal subunits and alters the UV absorbance spectrum of 70S ribosomes

We report a direct procedure to determine the proteins near the IF-3 binding site in purified 30S and 50S ribosomal subunits. This procedure introduces only limited numbers of cleavable crosslinks between IF-3 and its nearest neighbors. The cleavable crosslinking reagent, 2-iminothiolane, was used to crosslink IF-3 in place to both 30S and 50S subunits. Ribosomal proteins S9/S11, S12, L2, L5 and L17 were found, by this approach, to be in close proximity to the factor in purified IF-3-subunit complexes. In addition, IF-3 was shown to alter the ultraviolet absorbance spectrum of E. coli 70S ribosomes at 10 mM Mg2+. The magnitude of the observed difference spectrum at a constant IF-3/ribosome ratio of 1.0, is linearly dependent upon ribosome concentration over the range 5 nM - 55 nM. Titration experiments indicated that the observed effect is maximal at an IF-3/ribosome ratio of approximately 1.0. These results are taken to indicate a conformational change in the 70S ribosome induced by IF-3.

Fluorescence polarization studies of the interaction of Escherichia coli protein synthesis initiation factor 3 with 30S ribosomal subunits

Steady-state fluorescence polarization techniques were used to study the binding of initiation factor 3 (IF3) to 30S ribosomal subunits. Covalent fluorescent derivatives of IF3 were prepared by treating the pure protein with fluorescein isothiocyanate. The fluorescein-labeled IF3 (F-IF3) contained 0.8--1.7 dye molecules per protein. Polyacrylamide gel electrophoretic analysis of the derivatized forms is consistent with the view that the probe is randomly attached, presumably to lysine epsilon-amino groups. The activity of F-IF3 is not impaired in assays for binding to 30S ribosomal subunits or in promoting formylmethionyl-tRNA binding to 70S ribosomes. Fluorescence polarization values were measured at different F-IF3 and 30S ribosomal subunit concentrations, and the association constant and number of binding sites were calculated. In buffer containing 10 mM magnesium acetate and 100 mM ammonium chloride, the association constant is (3.1 +/- 1.4) x 10(7) M-1, and the number of ribosomal binding sites is 1.2 +/- 0.2. The value for the association constant varies inversely with the ammonium chloride and magnesium acetate concentrations by a small amount. Competition studies show that nonderivatized IF3 binds to 30S ribosomal subunits with the same affinity as F-IF3. Therefore, the association constants measured for F-IF3 are valid for IF3 as well.

Kinetic studies of the rates and mechanism of assembly of the protein synthesis initiation complex

Rate constants for a number of the assembly reactions involved in forming Escherichia coli ribosome initiation complexes have been measured. These reactions were monitored in a stopped-flow device in which Rayleigh scattering and fluorescence anisotropy were followed as a function of time. Fluorescence was induced by laser excitation modulated at 50 kHz. Aminoacyl-tRNA, initiation factor 3 (IF3), and 70S ribosomes were labeled with fluorescent probes. The light-scattering and fluorescence data show that the antiassociation model for IF3 function cannot be correct. IF3 can be considered to act as an effector in an allosteric model for ribosome function. Fluorescence anisotropy stopped-flow experiments provided rate constants for the binding of IF3 to both 30S subunits and to the intact 70S ribosome. Aminoacyl-tRNA's and nucleotide triplets appear to bind rapidly to 70S ribosomes and then a slow first-order conformational change occurs.

The effect of initiation factor IF-1 on the dissociation of 70-S ribosomes of Escherichia coli

By means of exchange studies, in which 3H-labelled 50-S subunits and unlabelled 70-S ribosomes from Escherichia coli MRE 600 were used, it has been demonstrated that the 30-S subunit is the only target for IF-3 in the dissociation of 70-S ribosomes. The interference of IF-3 with the dynamic equilibrium of 70-S in equilibrium 50-S + 30-S occurs by binding of the factor to the 30-S subunit. The 30-S-IF-3 complex in impaired in the association reaction, which implies that IF-3 is acting as an anti-association factor. The action of IF-1 is two-fold. Firstly IF-1 increases the rate of exhcange of the ribosomal subparticles in the 70-S ribosome without changing the position of the equilibrium. Thus the spontaneous equilibrium is attained more rapidly in the presence of IF-1. This kinetic effect of IF-1 is also demonstrated in the IF-3-mediated dissociation of 70-S ribosomes. Secondly IF-1 is able to increase the IF-3-mediated dissociation. It seems likely that the explanation for the latter phenomenon must be sought in the binding of IF-1 to 70-S ribosomes, resulting in a loosening of the ribosomes structure, as well as to 30-S. IF-3 complex, thaereby slowing down the association reactions of the subunits.

Reactivity of ribosomal sulfhydryl groups in 30S ribosomal subunits of Escherichia coli and 30S-IF-3 complexes

The reaction of 30S subunits with the SH group reagent N-ethylmaleimide (NEM) causes the loss of approximately 60% of their synethetic activity, but has little or no effect on the ribosomal binding of initiation factor IF-3. The ribosomal binding of this factor, on the other hand, was found to significantly influence the rate and the extent to which several 30S ribosomal proteins react with radioactively labeled NEM when the reaction kinetics of individual ribosomal proteins toward NEM were compared in 30S and 30S-IF-3 complexes. Of the nine 30S ribosomal proteins which react with NEM, proteins S1, S11, S12, and S18 were found to have lower reactivities, while proteins S4 and S21 displayed higher reactivity in the presence of IF-3. The reactivity of proteins S8, S13, and S17, on the other hand, appeared to be influenced little or not at all by the presence of the factor. These results are interpreted as supporting evidence for the premise that the binding of IF-3 results in a conformational change of the 30S subunit.

Recognition of initiation codons in modified f2 RNA by Escherichia coli ribosomes

f2 phage RNA treated with O-methylhydroxylamine under denaturing conditions loses its ordered structure with consequent exposure of the normally hidden initiation codons. In the presence of Escherichia coli ribosomes and crude initiation factors modified f2 RNA binds about 50 times more f-[3H]Met-tRNA than native f2 RNA. The interaction of native f2[14C]RNA with ribosomes requires initiation factors. The binding of O-methylhydroxylamine-modified f2 [14C]RNA to E. coli 70-S or 20-S ribosomes does not depend on the presence of initiation factors. A significant number of ribosomes deficient in initiation factors interact with a molecule of modified f2 [14C]RNA. Treatment of the resultant polysomal complex with pancreatic RNase yields ribosomes with f2 RNA fragments protected against RNase. Almost all AUG/GUG codons in the f2 RNA are located on the RNase-insensitive ribosome-bound fragments, constituting only 25% of the entire molecule. Addition of crude initiation factors to such ribosomes with fragments of modified f2 RNA promotes binding of f-[3H]Met-tRNA. The resultant complex is fully reactive with puromycin. No binding of Ac-Phe-tRNA takes place under similar conditions.

Mechanism of dissociation of ribosomes of Escherichia coli by initiation factor IF-3

Initiation factor IF-3 clearly can cause dissociation of ribosomes by binding to 30S subunits and thus shifting the spontaneous equilibrium, but it theoretically may also do so by binding to 70S ribosomes. Previously reported experiments with differentially labeled ribosomes and subunits seemed to eliminate the latter mechanism, but these experiments neglected a substantial decrease in the specific activity of the added subunits resulting from net dissociation of the ribosomes by IF-3. The present experiments eliminate or correct this effect. The results exclude direct action on 70S ribosomes as a significant mechanism of dissociation by IF-3.

Ribosomal subunit interaction as studied by light scattering. Evidence of different classes of ribosome preparations

The Mg2+-dependent equilibrium of ribosomal subunits was studied by light scattering in the absence of any other factor of protein synthesis. The difference of intensity in the light scattered by dissociated 30S-50S couples and by 70S particles was used as a method to measure the percentage of association as a function of Mg2+ under conditions of nonperturbation of the equilibrium. We found that pressure-resistant (type A) and non-pressure-resistant (type B) ribosomes may be characterized by the different behavior of their association equilibrium curves. The thermodynamic parameters of this equilibrium and their comparison for the two classes of ribosomes were calculated from experiments at different temperatures.

The irreversible step in formation of initiation complexes of Escherichia coli

At some stage during initiation the ribosomal subunits of Escherichia coli must become irreversibly coupled, since polysomal ribosomes, in contrast to free ribosomes, are not dissociated by initiation factor IF-3. To determine when irreversibility develops we have compared the response to IF-3 of mature, puromycin-reactive initiation complexes, made with GTP, and of intermediate, puromycin-unreactive complexes, made with GMPPCP. The latter complexes initially appeared to be dissociated by the factor but this effect was found to be due to artificial loss of the ligands at the Mg2+ concentration customary in the test for dissociation. At a slightly higher Mg2+ concentration (4 mM), sufficient to retain the ligands, the GMPPCP complexes were not significantly dissociated by IF-3, at concentrations that caused complex dissociation of free ribosomes. It thus appears that the intermediate 70S initiation complex, though less stable to ionic dissociation than the mature complex, is in effect irreversible under physiological conditions.

Effect of initiation factor 3 binding on the 30S ribosomal subunits of Escherichia coli

Under certain conditions, initiation factor 3 (IF-3) can cause the release of aminoacyl-tRNA bound to 30S ribosomal subunits of E. coli. It is shown that this IF-3-induced aminoacyl-tRNA release cannot be attributed to either nucleolytic attack or competition between IF-3 and aminoacyl-tRNA for the same ribosomal binding site. It was found that the 30S-aminoacyl-tRNA-codon complexes formed in the absence of IF-3 are intrinsically different from those prepared in the presence of IF-3. In the absence of IF-3, the ribosomal binding of aminoacyl-tRNA is a virtually irreversible process, since the bound aminoacyl-tRNA can neither be spontaneously released upon dilution nor exchanged for unbound aminoacyl-tRNA. In the presence of IF-3, the binding of one molecule of IF-3 per 30S ribosome renders the binding of aminoacyl-tRNA reversible upon dilution and promotes exchange between bound and unbound aminoacyl-tRNA. It is suggested that this difference is due to a conformational transition of the 30S ribosomal subunit induced by the binding of IF-3. The possible implications of this finding in relation to the mechanism of action of IF-3 and its functional role in the cell are discussed.