Isolation and Partial Characterization of Reticulocyte Factors M1 and M2

To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes

Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.

Increased levels of eIF2A inhibit translation by sequestering 40S ribosomal subunits

eIF2A was the first eukaryotic initiator tRNA carrier discovered but its exact function has remained enigmatic. Uncharacteristic of translation initiation factors, eIF2A is reported to be non-cytosolic in multiple human cancer cell lines. Attempts to study eIF2A mechanistically have been limited by the inability to achieve high yield of soluble recombinant protein. Here, we developed a purification paradigm that yields ∼360-fold and ∼6000-fold more recombinant human eIF2A from Escherichia coli and insect cells, respectively, than previous reports. Using a mammalian in vitro translation system, we found that increased levels of recombinant human eIF2A inhibit translation of multiple reporter mRNAs, including those that are translated by cognate and near-cognate start codons, and does so prior to start codon recognition. eIF2A also inhibited translation directed by all four types of cap-independent viral IRESs, including the CrPV IGR IRES that does not require initiation factors or initiator tRNA, suggesting excess eIF2A sequesters 40S subunits. Supplementation with additional 40S subunits prevented eIF2A-mediated inhibition and pull-down assays demonstrated direct binding between recombinant eIF2A and purified 40S subunits. These data support a model that eIF2A must be kept away from the translation machinery to avoid sequestering 40S ribosomal subunits.

Translation elongation factor P (EF-P)

Translation elongation factor P (EF-P) is conserved in all three domains of life (called eIF5A and aIF5A in eukaryotes and archaea, respectively) and functions to alleviate ribosome pausing during the translation of specific sequences, including consecutive proline residues. EF-P was identified in 1975 as a factor that stimulated the peptidyltransferase reaction in vitro but its involvement in the translation of tandem proline residues was not uncovered until 2013. Throughout the four decades of EF-P research, perceptions of EF-P function have changed dramatically. In particular, while EF-P was thought to potentiate the formation of the first peptide bond in a protein, it is now broadly accepted to act throughout translation elongation. Further, EF-P was initially reported to be essential, but recent work has shown that the requirement of EF-P for growth is conditional. Finally, it is thought that post-translational modification of EF-P is strictly required for its function but recent studies suggest that EF-P modification may play a more nuanced role in EF-P activity. Here, we review the history of EF-P research, with an emphasis on its initial isolation and characterization as well as the discoveries that altered our perceptions of its function.

A Retrospective on eIF2A-and Not the Alpha Subunit of eIF2

Initiation of protein synthesis in eukaryotes is a complex process requiring more than 12 different initiation factors, comprising over 30 polypeptide chains. The functions of many of these factors have been established in great detail; however, the precise role of some of them and their mechanism of action is still not well understood. Eukaryotic initiation factor 2A (eIF2A) is a single chain 65 kDa protein that was initially believed to serve as the functional homologue of prokaryotic IF2, since eIF2A and IF2 catalyze biochemically similar reactions, i.e., they stimulate initiator Met-tRNAi binding to the small ribosomal subunit. However, subsequent identification of a heterotrimeric 126 kDa factor, eIF2 (α,β,γ) showed that this factor, and not eIF2A, was primarily responsible for the binding of Met-tRNAi to 40S subunit in eukaryotes. It was found however, that eIF2A can promote recruitment of Met-tRNAi to 40S/mRNA complexes under conditions of inhibition of eIF2 activity (eIF2α-phosphorylation), or its absence. eIF2A does not function in major steps in the initiation process, but is suggested to act at some minor/alternative initiation events such as re-initiation, internal initiation, or non-AUG initiation, important for translational control of specific mRNAs. This review summarizes our current understanding of the eIF2A structure and function.

Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology

Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.

Ribosomes from aging mice are not generally deficient in cell-free protein synthesis

Cell-free protein synthesis by mouse liver ribosomes was examined as a function of the age of individual ribosome donors. In two strains of mouse, one long-lived and one short-lived, both the fraction of polyribosomes and the rate of in vitro ribosomal protein synthesis remained essentially constant throughout the lifespan, although in each "old" group one of three mice fell below the range of values observed for all other mice. Poly(U) stimulation of preincubated ribosome preparations similarly did not change with senescence; whereas poly(U)-directed synthesis by washed monosomes, pelleted after messenger run-off, increased two-fold for old mice. These results indicate that ribosomes of old mice are not necessarily defective in protein-synthesizing capacity, as previously reported, but may become defective in particular individuals.

A low molecular weight nuclear RNA from HeLa cells inhibits exogenous messenger RNA-dependent protein synthesis

A low molecular weight RNA of nuclear origin from adenovirus-infected HeLa cells inhibited rabbit reticulocyte polyribosomal RNA-dependent cell-free protein synthesis by reducing th formation of 80 S ribosome from 40 S-mRNA complex and 60 S subunits. This inhibitor did not hybridize with intact or HindIII-digested fragments of the viral DNA. Therefore it appears to be a 5.5 S RNA of cellular origin, which binds significantly with authentic IF-M2B from rabbit reticulocytes. In all these characteristics the inhibitor appears identical to a similar 5.5 S inhibitor RNA from non-infected HeLa cells.

Rate-limiting factors for lymphocyte protein synthesis. Ribosome commitment and the capacity of lymphocyte cell-free systems to translate exogenous mRNAs

The properties of the protein synthesising systems of different lymphocyte preparations have been compared with those of non-lymphoid tissues. Polysome profiles from rat thymocytes, sheep mesenteric lymphocytes, rat liver and mouse ascites tumours showed that the commitment of ribosomes to protein synthesis in lymphocytes was relatively low. Initiation factor activities, assessed on the abilities of post-mitochondrial fractions to support exogenous mRNA translation, were limited or undetectable in lymphoid tissues. While the thymocyte system translated globin mRNA, the response was enhanced by ascites extracts rich in initiation factors. The mesenteric lymphocyte system responded only marginally to globin mRNA and poly(U) but the responses were not enhanced by ascites extracts. The activity of isolated mesenteric ribosomes was comparable with ribosomes from other tissues, indicating that extraribosomal factors were responsible for the poor overall activity of the mesenteric system. Finally, the effects of cycloheximide on the recruitment of polysomes in lymphocytes indicated that the commitment of ribosomes to protein synthesis might be restricted by both limited mRNA availability and limited capacity for initiation of mRNA translation.

Activity of protein synthesis initiation factors in cytosol from rat liver and muscle and ascites cells

The decrease induced by appropriate initiation factors in [Mg] required for optimal polyphenylalanine synthesis primed by poly(U) has been used as an assay to test for the presence of these factors in cytosol of rat liver and muscle and of ascites cells. By calculation and from changes in [Mg] optima on addition of phosphoenolpyruvate and phosphocreatine, the [Mg2+] as opposed to total [Mg] required for polyphenylalanine synthesis has been determined. Contrary to a previous report, factors necessary for polyphenylalanine synthesis at low [Mg] appear to be present in cytosol of muscle and liver as well as that from ascites cells. The significance of these finding in relation to distribution of specific initiation factors is discussed.

Stimulation of protein synthesis and Met-tRNAf binding by phosphorylated sugars: studies on their mechanism of action

It has been previously reported by J. R. Lenz et al. [(1978) Biochemistry 17, 80--87] that certain phosphorylated sugars stimulate protein synthesis in extracts of mammalian cells. This effect was found to be due to a stimulation of Met-tRNAf binding to 40S ribosomal subunits, both in whole extracts and with isolated ribosomes. However, formation of a ternary complex of Met-tRNAf, initiation factor eIF-2, and GTP was not stimulated. It was also shown that the stimulation is not due solely to metabolism of the sugars. The present communication further characterizes the stimulatory effect of the sugars. They were found to prevent the inactivation of ribosomes that occurs during protein synthesis incubations. The sugars were also found to inhibit cAMP-dependent protein kinases noncompetitively. However, they stimulate Met-tRNAf binding to 40S ribosomal subunits even under conditions in which an inhibition of protein kinase has no effect. Although it has bot been possible to demonstrate a direct association of the sugars with the 40S initiation complex, the evidence suggests that their effect is mediated by an interaction with one of the components involved in the formation of this complex.

Activity of partially purified protein chain initiation factors from the livers of dimethylnitrosamine-treated rats

Partially purified polypeptide chain initiation factors were prepared from the 0.5 M KCl wash of rat liver microsomes. Their activities in connection with dimethylnitrosamine (DMNA)-induced inhibition of protein synthesis were studied by use of the following reactions: (1) poly(U)-directed binding of Phe-tRNA to ribosomes, (2) formation of a GTP-dependent ternary initiation complex with Met-tRNAf, (3) binding of Met-tRNAf to 40-S ribosomal subunits, (4) assembly of a Met-tRNAf containing 80-S ribosomal initiation complex and (5) ribosome-dependent GTPase activity. The inhibition of protein synthesis with DMNA was not associated with a loss of factor activity in any of these reactions. In the binding of Met-tRNAf to 40-S subunits there was a noticeable increase, probably related to the stability of the resulting complex. The Met-tRNA deacylase activity was also increased.

Accumulation of tRNAMetf on 80-S ribosomes in vitro under the influence of a Met-tRNA deacylase from rat-liver microsomes

A Met-tRNA deacylase has been partially purified from the 0.5 M KCl wash of rat liver microsomes. In preparative sucrose gradients, the active component sediments as a single band at about 6 S, corresponding to an estimated molecular weight of 1.7 X 10(5). The deacylase is specific for Met-tRNA, without discriminating between Met-tRNA f and Met-tRNAm. Met-tRNAf bound to the initiation factor IF-MP in the ternary complex, IF-MP-GTP-Met-tRNAf, or to initiation-factor-dependent, complexes with 40-S subunits or 80-S ribosomes, is protected against deacylation. However, in the course of the initiation-factor-dependent joining of the 40-S subunit complex to 60-S ribosomal subunits, the bound Met-tRNAf is exposed to added deacylase. Under these conditions, deacylation is inhibited by GTP. The tRNAMetf remains bound and accumulates on the 80-S ribosomes.

Evidence for role of m7G5'-phosphate group in recognition of eukaryotic mRNA by initiation factor IF-M3

7-methylguanosine 5'-monophosphate inhibits protein synthesis in a fractionated, messenger-dependent, reticulocyte cell-free system. This compound also inhibits binding of histone mRNA to reticulocyte ribosomes as well as interaction of VSV mRNA and histone mRNA but not EMC virus RNA with purified initiation factor IF-M3. These studies provide evidence that the role of 7-methylguanosine in the mechanism for initiation of eukaryotic mRNA translation may be related to specific recognition of mRNA by initiation factor IF-M3.

Inhibitory action of different RNA fractions on the translation of globin mRNA in vitro

Preparations of 28S rRNA and 12S RNA, obtained from sheep lymphocytes, were shown to inhibit the translation of globin mRNA. An inhibition by a given amount of 12S or 28S RNA was only obvious at saturating or near saturating levels of globin mRNA, suggesting that the inhibitory RNAs interacted with some factor essential for protein synthesis other than mRNA. The inhibitory RNAs had no effect on the translation of the synthetic template polyuridylic acid. It is suggested therefore that the target for inhibitory RNAs might be a natural mRNA specific initiation factor.

Translation of murine leukemia virus RNA in cell-free systems from animal cells

The virion RNA of Moloney murine leukemia virus (MuLV) has been translated in eukaryotic cell-free systems derived from mouse L- and human HeLa cells. In both systems at least three polypeptides, approximately 60,000, 70,000, and 180,000 in apparent molecular weight, were formed in response to the added 35S MuLV RNA. All three polypeptides were precipitable with antiserum to detergent-disrupted MuLV. Fingerprint analysis of tryptic digests indicated that all three contain anino acid sequences in common with each other and with the major methionine-containing structural proteins of the virion.

Antibiotics and compounds affecting tanslation by eukaryotic ribosomes. Specific enhancement of aminoacyl-tRNA binding by methylaxnthines

The mode and site of action of inhibitors of translation (initiation, elongation and termination of protein synthesis) in eukaryotic systems is reviewed. The isolation and characterization of a factor is described that binds Ac-Phe-tRNA to form a complex made up of binding factors, Ac-Phe-tRNA, and ribosome. The binding of Ac-Phe-tRNA probably occurs at the ribosomal site involved in the binding of the initiator substrate Met-tRNAF. The effect of inhibitors of the intitiation phase of protein synthesis on the nonenzymic Ac-Phe-tRNA binding to ribosomes is investigated. The two sites translocation model for translation in eukaryotic cells is presented and the effects of inhibitors on the various steps of protein synthesis are determined empirically. The site of action of inhibitors of peptide bond formation at the ribosomal peptidyl transferase center is elucidated. The action of inhibitors of translocation is sutdied in model cell-free systems from human cells. In addition, a number of methylxanthines are shown to enhance the elongation phase in polypeptide synthesis by stimulating the enzymic binding of aminoacyl-tRNA. The effect of caffeine, theophylline and its derivatives are shown to be fairly specific and dependent on the ribosome concentration. Aminophylline is shown to have a similar effect but also enhances aminoacyl-tRNA synthetase activity at low Mg++ concentrations, probably displacing the optimal concentration of Mg++ in the reaction. This second effect of aminophylline appears to be due to the ethylenediamine moiety of aminophylline since it is also observed in the presence of different polyamines but not in the presence of caffeine or theophylline.

Isolation of two protein factors from maize involved in poly U-dependent polyphenylalanine synthesis by maize ribosomes

Two protein factors, isolated from S-100 of maize shoots, were found to be required not only for a "Mg(2+) shift" for poly U-dependent polymerization of phenylalanine, but also for polyphenylalanine synthesis. They seem to be crude preparations of EF-1 and EF-2. The poly U-directed amino acid incorporation by washed ribosomes was completely dependent upon these factors.

Protein chain initiation in vitro by liver cell components from DMNA-treated rats

The mechanism of inhibition of protein synthesis in rat liver after dimethylnitrosamine (DMNA) administration was studied at the level of peptide-chain initiation by use of initiation-dependent amino acid incorporating systems. Ribosomal monomers, poly(A)-concontaining loss of acticity due to the DMNA treatment. The poly(A) RNA from monosomes and polysomes, and crude initiation factors from microsomes were prepared 2 h after a single dose of DMNA (75 mg/kg), and their activities in the production of new protein chains determined under conditions of nearly linear response. Monosomes and crude initiation factors from DMNA-treated rats were at least as active as those from controls. Preparations of poly(A)-containing RNA had a consistently higher template activity when prepared from polysomes instead of monosomes. However, in neither case was there any ltaining RNA was methylated by DMNA to about the same extent as the 18S and 28S rRNA. The methylation was consistently somewhat higher in the RNA preparations from monosomes than in those from polysomes.

Activation and inactivation of genes determining hemoglobin types.20s

Globin gene switching in sheep and goats has been used as a model system for examining gene expression in differentiating red blood cells. Sheep and goats switch from the synthesis of hemoglobin A to hemoglobin C in response to erythropoietin. The regulatory mechanism producing this switch in hemoglobin types could occur at the cellular, nuclear, or cytoplasmic level. Evidence is presented which suggests that regulation is occurring, in fact, at the nuclear level. Sheep and goat erythroid colonies have been grown in plasma clot culture in order to study the synthesis of individual globin chains. Erythropoietin is required for colony formation. The switch from hemoglobin A to hemoglobin C synthesis requires not only colony formation but also a higher concentration of erythropoietin than is required just for the production of colonies. A cell-free transcriptional system using bone marrow chromatin and mammalian DNA-dependent RNA polymerase has been developed in order to examine the nuclear control mechanisms in more detail.

Binding of Met-tRNA-f to native and derived 40S ribosomal subunits

Our previous work has shown that the native 40S ribosomal subunits (those found free in the cell sap) but not polyribosomal 40S subunits have additional associated proteins that are removed by 0.5 M KCl. In this communication we present evidence that in the Ehrlich cell one of the native subunit associated proteins is the mammalian initiation factor that forms a Met-tRNA-f-factor-GTP complex, and is required for the binding of Met-tRNA-f to the 40S subunit. Initial examination of the KCl wash of the Ehrlich cell total ribosomal pellet revealed a factor which (1) shifted the elution of Met-tRNA-f and of GTP from the included to the excluded volume on Sephadex G-100 chromatography, (2) stimulated the binding of Met-tRNA-f to Millipore filters, and (3) stimulated the binding of Met-tRNA-f to salt-washed 40S subunits. These activities were dependent upon or enhanced by GTP; were inhibited by GDP; were much greater for Met-tRNA-f than for Met-tRNA-m or for lysyl-tRNA; and were concentrated in the KCl ribosomal wash and were not detected in the cell soluble fraction. Met-tRNA-f bound in conjunction with a specific amount of KCl wash protein, to form a distinctive particle of bouyant density 1.40 g cm minus 3 in CsCl, identical in density to one form of the native 40S subunit. Native 40S subunits, but no other subunits, contained a factor which was eluted by 0.5 M KCl and which (1) stimulated the binding of Met-tRNA-f to Millipore filters, and (2) stimulated the binding of Met-tRNA-f to salt-washed 40S subunits. The factor appeared to be localized on the native 40S subunit of density 1.40 g cm minus 3.