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.     

Temperature sensitivity of protein synthesis initiation. Inactivation of a ribosomal factor by an inhibitor formed at elevated temperatures.

When a reticulocyte lysate, supplemented with hemin, was warmed at 42 °C, its protein-synthesizing activity was greatly decreased. This was accompanied by the reduced formation of the 40 S·Met-tRNA_f initiation complex. This complex preformed at 34 °C, however, was stable and combined with added globin mRNA and the 60 S ribosomal subunit to form the 80 S complex at the elevated temperature. When the ribosome-free supernatant fraction of lysates was warmed at 42 °C with hemin and then added to the fresh lysate system, it inhibited protein synthesis by decreasing the formation of the 40 S complex. This decrease in protein synthesis by warmed lysates or warmed supernatant could be overcome by high concentrations of GTP and cyclic AMP. This effect of GTP and cyclic AMP was antagonized by ATP. The results indicate that the inactivation of protein synthesis by the lysate warmed at 42 °C is due to the formation of an inhibitor in the supernatant. The ribosomal KCl extract prepared from the lysate that had been warmed at 34 °C and then incubated at this temperature for protein synthesis supported protein synthesis by the KCl-washed ribosome at both 34 and 42 °C. On the contrary, the extract from lysates that had been warmed at 42 °C and then incubated at 34 °C could not support protein synthesis at 42 °C, although it was almost equally as promotive as the control extract in supporting protein synthesis at 34 °C. The results indicate that the factor which can protect protein synthesis against inactivation at 42 °C is itself inactivated in lysates warmed at 42 °C. However, the activity of this extract to support formation of the ternary complex with Met-tRNA_f and GTP was not reduced. Native 40 S ribosomal subunits isolated from lysates that had been warmed at 42 °C and then incubated for protein synthesis indicated that the quantity of subunits of density 1.40 g/cm³ in a CsCl density gradient were decreased while those of density 1.49 g/cm³ were increased. The factor-promoted binding of Met-tRNA_f to the 40 S subunit of lower density from the warmed and unwarmed lysates was equal, suggesting that the ribosomal subunit was not inactivated. These results were discussed in terms of the action of the inhibitor formed in the supernatant at 42 °C, which may inactivate a ribosomal factor essential for protein synthesis initiation.     

Fluoride inhibition of the initiation of protein synthesis in the reticulocyte lysate cell-free system.

KF (30 mM) strongly inhibits polypeptide chain initiation in the reticulocyte lysate cell-free system.. Chain elongation is partially inhibited but proceeds to a significant extent with little initiation of new chains. Polysome breakdown is incomplete after incubations as long as 20 min. Under these conditions deacylated tRNA-Met accumulates in a fraction sedimenting faster than 120 S and thus may be associated with ribosomes bound to mRNA. Incubation of the system with KF results in the accumulation of a complex which can initiate synthesis of polypeptide chains in the presence of aurintricarboxylate; KF thus inhibits a step in initiation after that inhibited by aurintricarboxylate. The accumulation of deacylated tRNA-Met is correlated with the accumulation of the aurintricarboxylate-resistant complex. Both phenomema are dependent on KF and both are inhibited by aurintricarboxylate in the same range of concentrations which inhibit initiation of protein synthesis.     

The binding of Met-tRNAf to isolated 40-S ribosomal subunits and the formation of Met-tRNAf - 80-S-ribosome initiation complexes.

Different forms of 40-S ribosomal subunit, distinguishable by their buoyant densities on CsCl equilibrium density gradients, are formed when derived 40-S ribosomal subunits are incubated with partially purified reticulocyte ribosomal wash proteins. One of these subunits, the 1.37-g-cm-3 form is not present in the cell but the other two forms, the 1.40-g-cm-3 and 1.40-g-cm-3 subunits, are present in cell extracts. 35S label is bound to 1.37-g-cm-3 and 1.40-g-cm-s subunits when [35S]Met-tRANf, GTP and poly(A,U,G) are included in the incubations. The 35S-labelled 40-S subunits recovered, and the amount of 35S label bound to them, are changed if the [35S]Met-tRNAf-40-S-subunit-poly(A,U,G) complexes are first purified on sucrose gradients before analysing them on CsCl. The 1.37-g-cm-3 particle is no longer seen and the total quantity of 35S label on the 40-S subunits is 90% lower after sucrose gradient purification. Between 30% and 40% of the 40-S subunits bind [35S]Met-tRNAf when 1 mM GTP, an excess of ribosomal wash proteins and [35S]Met-tRNAf over derived 40-S subunits, and poly(A,U,G) or AUG is included in the incubations. The omission of poly(A,U,G) or AUG from the incubations substantially lowers the amount of subunit-bound 35S label ultimately recovered. With these incubations less than 10% of the 40-S subunits have bound [35S]Met-tRNAf. [35S]Met-tRNAf binding is affected by the nature of the RNA added. The addition of poly(U), rRNA and native 9-S golbin mRNA is without effect, whereas denatured globin mRNA is stimulatory. Maximum binding is obtained however with AUG. Poly(A,U,G) is less stimulatory than AUG but more stimulatory than denatured mRNA, suggesting that the number as well the accessibility of the AUG initiations condons determines the amount of 35S label bound. Similar results are obtained for the ribosomal-wash-dependent binding of [35S]Met-tRNAf to 80-S ribosomes. Contrary to the binding results, the ability of mRNA to stimulate protein synthesis is dependent on the integrity of the mRNA. Thus, native 9-S globin mRNA but not poly(A,U,G) stimulatex protein synthesis in the wheat germ system. HCHO-treated globin mRNA, although stimulatory, is 45% less effective than native mRNA. The addition of AUG, derived 60-S subunits and extra ribosomal wash is required for the formation of [35S]Met-tRNAf-80-S-ribosome complexes from sucrose-gradient-purified [35S]Met-tRNAf-40-S-subunit complexes. The 80-S ribosome complexes are able to form peptide bonds. Thus, if puromycin is added to the full incubations at zero time, no 35S label is present on the 80-S ribosome. 35S label is released as methionyl-puromycin. If the [35S]Met-tRNAf-40-S-subunit complexes are assembled with poly(A,U,G) or AUG in the incubations and then purified, only derived 60-S subunits are required to form [35S]Met-tRNAf-80-S-ribosome complexes. 35S label is not released from them when puromycin is added to the incubations unless extra ribosomal wash is also added.     

The human translation initiation multi-factor complex promotes methionyl-tRNAi binding to the 40S ribosomal subunit

The delivery of Met-tRNA(i) to the 40S ribosomal subunit is thought to occur by way of a ternary complex (TC) comprising eIF2, GTP and Met-tRNA(i). We have generated from purified human proteins a stable multifactor complex (MFC) comprising eIF1, eIF2, eIF3 and eIF5, similar to the MFC reported in yeast and plants. A human MFC free of the ribosome also is detected in HeLa cells and rabbit reticulocytes, indicating that it exists in vivo. In vitro, the MFC-GTP binds Met-tRNA(i) and delivers the tRNA to the ribosome at the same rate as the TC. However, MFC-GDP shows a greatly reduced affinity to Met-tRNA(i) compared to that for eIF2-GDP, suggesting that MFC components may play a role in the release of eIF2-GDP from the ribosome following AUG recognition. Since an MFC-Met-tRNA(i) complex is detected in cell lysates, it may be responsible for Met-tRNA(i)-40S ribosome binding in vivo, possibly together with the TC. However, the MFC protein components also bind individually to 40S ribosomes, creating the possibility that Met-tRNA(i) might bind directly to such 40S-factor complexes. Thus, three distinct pathways for Met-tRNA(i) delivery to the 40S ribosomal subunit are identified, but which one predominates in vivo remains to be elucidated.     

Site-specific cleavage of the 40S ribosomal subunit reveals eukaryote-specific ribosomal protein S28 in the subunit head

After resolving the crystal structure of the prokaryotic ribosome, mapping the proteins in the eukaryotic ribosome is a challenging task. We applied RNase H digestion to split the human 40S ribosomal subunit into head and body parts. Mass spectrometry of the proteins in the 40S subunit head revealed the presence of eukaryote-specific ribosomal protein S28e. Recombinant S28e was capable of specific binding to the 3′ major domain of the 18S rRNA (K_a = 8.0 ± 0.5 × 10⁹ M⁻¹). We conclude that S28e has a binding site on the 18S rRNA within the 40S subunit head.

Structured summary

MINT-8044084: S8 (uniprotkb:P62241) and S19 (uniprotkb:P39019) colocalize (MI:0403) by cosedimentation through density gradient (MI:0029)MINT-8044095: S8 (uniprotkb:P62241), S19 (uniprotkb:P39019) and S13 (uniprotkb:P62277) colocalize (MI:0403) by cosedimentation through density gradient (MI:0029)MINT-8044024: S29 (uniprotkb:P62273), S28 (uniprotkb:P62857), S21 (uniprotkb:P63220), S20 (uniprotkb:P60866), S26 (uniprotkb:P62854), S25 (uniprotkb:P62851), S12 (uniprotkb:P25398), S17 (uniprotkb:P08708), S19 (uniprotkb:P39019), S14 (uniprotkb:P62263), S16 (uniprotkb:P62249) and S11 (uniprotkb:P62280) colocalize (MI:0403) by cosedimentation through density gradient (MI:0029)MINT-8044065: S29 (uniprotkb:P62273), S28 (uniprotkb:P62857), S19 (uniprotkb:P39019), S14 (uniprotkb:P62263) and S16 (uniprotkb:P62249) colocalize (MI:0403) by cosedimentation through density gradient (MI:0029)     

The alpha and gamma subunits of initiation factor eIF-2 can be cross-linked to 18S ribosomal RNA within the quaternary initiation complex, eIF-2.Met-tRNAf.GDPCP.small ribosomal subunit.

Initiation factor eIF-2 from rat liver was reacted with the hetero-bifunctional cross-linking reagents ABAI or APTPI without diminishing its ability to form the quaternary initiation complex with Met-tRNAf, GDPCP and the small ribosomal subunit. Upon irradiation with UV light, subunits alpha and gamma of eIF-2 became covalently linked to 18S ribosomal RNA. The subunits were identified electrophoretically after isolation of the covalent protein-rRNA complexes and subsequent degradation of the rRNA by nuclease and alkali treatments. The close proximity of the two factor subunits to sequences of ribosomal RNA within the quaternary complex could be confirmed in a second set of experiments using unmodified, 125I-labeled factor and diepoxybutane as cross-linking reagent.     

Electron microscopic study of eukaryotic 40S initiation complex in protein synthesis

This electron microscopic study demonstrates that formation of a functional eukaryotic 40S initiation complex is accompanied by conformational changes which obscure the characteristic structural features of the 40S ribosomal subunits and of the initiation factor eIF-3, the only macromolecular components of the complex individually resolvable by conventional high resolution electron microscopy. The complex, characterized by a sedimentation coefficient of 46S, appears as a globular particle with a diameter of about 280 A and several characteristic protrusions and incisions. Similar structures were obtained with [40S X eIF-3] initiation complexes formed by interaction of eIF-3 from rabbit reticulocytes with 40S ribosomal subunits from either A. salina cysts or mouse liver. Incubation of eIF-3 with prokaryotic 30S subunits from E. coli produced no [30S X eIF-3] structures. The binding of eIF-3 to 40S subunits is weak, and both the [40S X eIF-3] and the complete 40S initiation complexes have to be stabilized by glutaraldehyde fixation. The extensive conformational changes associated with the complex formation preclude direct electron microscopic localization of eIF-3, a globular protein approximately 100 A in diameter, in the initiation domain of the 40S subunit.     

Two-step purification of the major phosphorylated protein in reticulocyte 40S ribosomal subunits

In reticulocytes, a single ribosomal protein, S13, has been shown to be phosphorylated by the cAMP-regulated protein kinases. The 40S ribosomal subunits were phosphorylated in vitro with [gamma-32P]ATP to facilitate the identification of S13 during the two-step purification procedure. Total ribosomal protein from the 40S subunit was fractionated by phosphocellulose chromatography in urea, and S13 was purified to homogeneity by gel filtration on Sephadex G-100. The protein was identified by the radioactive phosphate, by molecular weight, and by the migration characteristics in a two-dimensional polyacrylamide gel electrophoresis system. Thin-layer electrophoresis of partial acid hydrolysates of S13 showed that more than one phosphorylated residue was present in the same oligopeptide, indicating at least some of the phosphoryl groups were clustered in the protein molecule.     

Function of eukaryotic initiation factor 5 in the formation of an 80 S ribosomal polypeptide chain initiation complex.

Eukaryotic initiation factor 5 (eIF-5), isolated from rabbit reticulocyte lysates, is a monomeric protein of 58-62 kDa. The function of eIF-5 in the formation of an 80 S polypeptide chain initiation complex from a 40 S initiation complex has been investigated. Incubation of the isolated 40 S initiation complex (40 S.AUG.Met.tRNAf.eIF-2 GTP) with eIF-5 resulted in the rapid and quantitative hydrolysis of GTP bound to the 40 S initiation complex. The rate of this reaction was unaffected by the presence of 60 S ribosomal subunits. Analysis of eIF-5-catalyzed reaction products by gel filtration indicated that both eIF-2.GDP binary complex and Pi formed were released from the ribosomal complex whereas Met-tRNAf remained bound to 40 S ribosomes as a Met-tRNAf.40 S.AUG complex. Reactions carried out with biologically active 32P-labeled eIF-5 indicated that this protein was not associated with the 40 S.AUG.Met-tRNAf complex; similar results were obtained by immunological methods using monospecific anti-eIF-5 antibodies. The isolated 40 S.AUG.Met-RNAf complex, free of eIF-2.GDP binary complex and eIF-5, readily interacted with 60 S ribosomal subunits in the absence of exogenously added eIF-5 to form the 80 S initiation complex capable of transferring Met-tRNAf into peptide linkages. These results indicate that the sole function of eIF-5 in the initiation of protein synthesis is to mediate hydrolysis of GTP bound to the 40 S initiation complex in the absence of 60 S ribosomal subunits. This leads to formation of the intermediate 40 S.AUG.Met-tRNAf and dissociation of the eIF-2.GDP binary complex. Subsequent joining of 60 S ribosomal subunits to the intermediate 40 S.AUG.Met-tRNAf complex does not require participation of eIF-5. Thus, the formation of an 80 S ribosomal polypeptide chain initiation complex from a 40 S ribosomal initiation complex can be summarized by the following sequence of partial reactions. (40 S.AUG.Met-tRNAf.eIF-2.GTP) eIF-5----(40 S.AUG.Met-tRNAf) + (eIF-2.GDP) + Pi (1) (40 S.AUG.Met-tRNAf) + 60 S----(80 S.AUG.Met-tRNAf) (2) 80 S initiation complex.     

Protein synthesis in rabbit reticulocytes: requirements for Met-tRNAf . 40S preinitiation complex formation with AUG-codon and physiological mRNAs

Under standard conditions, in the presence of GTP, highly purified eIF-2 and Co-eIF-2 factor preparations efficiently stimulated AUG-codon dependent but not physiological mRNA-dependent Met-tRNAf binding to 40S ribosomes. Replacement of GTP by a nonhydrolyzable GTP analog, GMP-PNP, in the above system, gave significant stimulation of Met-tRNAf binding to 40S ribosomes dependent on physiological mRNAs. Lower but significant stimulation of Met-tRNAf binding to 40S ribosomes was also observed when GTP was used in the presence of nucleoside 5'-diphosphate kinase (NDK) and ATP. ATP alone in the absence of NDK had no significant effect. This is the first report on the formation of a stable Met-tRNAf . 40S initiation complex dependent on physiological mRNAs and the factor requirements for such complex formation.     

Cross-linking of Met-tRNAf to eIF-2 beta and to the ribosomal proteins S3a and S6 within the eukaryotic inhibition complex, eIF-2 .GMPPCP.Met-tRNAf.small ribosomal subunit.

In the quaternary initiation complex, eIF-2.GMPPCP.Met-tRNAf.40S ribosomal subunit, the Met-tRNAf can be cross-linked to the beta subunit of initiation factor eIF-2 as well as to ribosomal proteins S3a and S6 by treatment with the bifunctional reagent, diepoxybutane. Using 40S subunits, modified in advance with the heterobifunctional reagent, methyl-rho-azido-benzoylaminoacetimidate, Met-tRNAf is covalently bound to the same ribosomal proteins (S3a and S6) upon irradiation of the complex with ultraviolet light. Under both conditions proteins S3a and S6, together with a limited number of other ribosomal proteins, are covalently bound to 18S ribosomal RNA.     

Substitution of selenocysteine for cysteine in a reticulocyte lysate protein synthesis system

Selenocysteine occurs in the peptide backbone of several selenoenzymes. The mechanism, of selenocysteine incorporation has not been well characterized. The incorporation of selenocysteine into protein in a rabbit reticulocyte lysate (RRL) was studied at high levels of selenocysteine. [⁷⁵Se]Selenocysteine incorporation was inhibited by cycloheximide and by nuclease treatment. Random RNA copolymers were tested for protein synthesis activity in the messenger RNA-dependent RRL system. Of the active polymers, poly CIU and GU most strongly stimulated the incorporation of selenocysteine. In a series of four polymers with different ratios of U to G, incorporation of selenocysteine and cysteine increased with increasing percentages of U, suggesting that selenocysteine and cysteine responded to the same codon, presumably UGU. Of the 20 protein amino acids, only cysteine and cystine competed with selenocysteine incorporation. Selenocysteine was charged to cysteine-accepting tRNA in RRL. These results show that at supraphysiological concentrations selenocysteine can substitute for cysteine in RRL protein synthesis. Misincorporation of selenocysteine could be important when animal tissues contain high levels of selenium.     

Involvement of ribosomal protein S1 in the assembly of the initiation complex.

Antibodies against ribosomal protein S1 (anti-S1) have been used to determine the function of S1 in the partial reactions involved in the translation of MS2 RNA in vitro. Vacant ribosomes are fully sensitive to the antibodies, whereas elongating ribosomes are resistant. We have determined at which stage of translation the resistance to anti-S1 is acquired. We find that insensitivity to anti-S1 already arises upon mixing 30-S subunits with MS2 RNA. Apparently the two particles form a complex in which S1 is functionally protected against its antibody. Complex formation depends on elevated temperature, a suitable ionic environment and it is stimulated by the initiation factor IF-3. It does not depend on IF-1, IF-2 or fMet-tRNA. Thus ribosomes have the potential to recognize the messenger in the absence of fMet-tRNA. Protein S1 appears directly involved in this primary recognition reaction.     

Dual effects of the ricin A chain on protein synthesis in rabbit reticulocyte lysate. Inhibition of initiation and translocation

Ricin A chain caused inhibition of protein synthesis by reticulocyte lysate with concomitant depurination of 28S rRNA. The partial reaction(s) of protein synthesis inhibited was investigated by following the appearance of [35S]methionine from initiator [35S]Met-tRNA into 40S ribosomal subunits, 80S monosomes and polysomes. Ricin A chain caused an accumulation of [35S]Met in monosomes which did not enter polysomes. In these respects the effects of the ricin A chain resembled those of diphtheria toxin, an inhibitor of elongation-factor-2-catalyzed translocation. This is consistent with the previously proposed site of action of ricin as an inhibitor of elongation. However, the inhibitory effects of the ricin A chain and diphtheria toxin are not equivalent because we observed that the rate of formation of the 80S initiation complex was reduced approximately sixfold with the ricin A chain relative to diphtheria toxin. Analysis of methionine-containing peptides bound to 80S monosomes in ricin-A-chain-inhibited and diphtheria-toxin-inhibited lysates, programmed with globin mRNA, revealed a predominance of Met-Val, suggesting that the elongation cycle is inhibited at the translocation step. Translocation was also implicated as the step blocked in both the ricin-A-chain-inhibited and diphtheria-toxin-inhibited lysates, by the finding that nascent peptide chains were unreactive towards puromycin. It is concluded that ricin-A-chain-modified ribosomes are deficient in two protein synthesis partial reactions: the formation of the 80S initiation complex during initiation and the translocation step of the elongation cycle.     

The spatial arrangement of the complex between eukaryotic initiation factor eIF-3 and 40 S ribosomal subunit. Cross-linking between factor and ribosomal proteins

The binding site for eIF-3 on the small ribosomal subunit was studied (a) by use of a complex of eIF-3 and derived 40 S ribosomal subunit from rat liver, and (b) by use of native small ribosomal subunits from rabbit reticulocytes. After treatment of both complexes with dimethyl 4,7-dioxo-5,6-dihydroxy-3,8-diazadecanbisimidate ribosomal proteins S3a, S4, S6, S7, S8, S9, S10, S23/24 and S27 became covalently linked to eIF-3 and were isolated together with the factor by gradient centrifugation. The ribosomal proteins were identified by two-dimensional polyacrylamide gel electrophoresis after periodate cleavage of the link(s).