Tobacco Mosaic Virus Ribonucleic Acid-dependent Amino Acid Incorporation in a Wheat Embryo System in Vitro

Binding of ATP and messenger RNA by the beta-subunit of eukaryotic initiation factor 2

In addition to forming a ternary complex with Met-tRNA(f) and GTP, eukaryotic initiation factor 2 (eIF-2) recognizes a specific site in mRNA molecules. Both binding activities are regulated by ATP, which itself binds tightly and specifically to eIF-2. Denaturation of eIF-2 with urea leads to complete loss of Met-tRNA(f) binding activity, while mRNA binding activity is stable. Hence, distinct conformational features in eIF-2 are required for ternary complex formation and for binding of mRNA. Chromatography of eIF-2 over ATP-agarose, in denaturing conditions that induce polypeptide subunit dissociation, results in selective retention of the beta-subunit of eIF-2. Isolated beta-subunit is capable of binding mRNA as well as ATP. Cibacron blue 3G-A binds tightly to eIF-2 and inhibits the binding of mRNA. This inhibition is relieved upon addition of ATP, showing that Cibacron blue 3G-A competes with ATP for eIF-2. eIF-2 beta subunit, active in binding of mRNA, is recovered upon chromatography of eIF-2 in denaturing conditions over matrix-bound Cibacron blue 3G-A. These results show that the ability of eIF-2 to bind mRNA and its ability to bind ATP are both lodged within remarkably stable domains of its beta-subunit. During initiation of protein synthesis, the eIF-2 beta subunit may thus interact with three ligands important for translational control: Met-tRNA(f), mRNA and ATP.

Protein synthesis in yeast Saccharomyces cerevisiae. Purification of Co-eIF-2A and 'mRNA-binding factor(s)' and studies of their roles in Met-tRNAf.40S.mRNA complex formation

Antibodies prepared against a homogeneous preparation of Co-eIF-2A20 [Ahmad et al. (1985) J. Biol. Chem. 260, 6955-6959] reacted with several polypeptides including an 80-kDa polypeptide present in a crude yeast ribosomal salt wash. This 80-kDa polypeptide, containing Co-eIF-2A (Co-eIF-2A80) activity, has been extensively purified using a two-step purification procedure involving an immunoaffinity column chromatograph prepared using antibodies against Co-eIF-2A20 (fraction II) and hydroxyapatite chromatography (fraction III). The factors, eIF-2 + homogeneous Co-eIF-2A80 (fraction III) promoted Met-tRNAf.40S complex formation with an AUG codon but not with a physiological mRNA or a polyribonucleotide messenger poly(U,G) whereas eIF-2 + a partially purified Co-eIF-2A80 preparation (fraction II) promoted Met-tRNAf.40S complex formation with an AUG codon as well as with globin mRNA and poly(U,G) messenger. This factor-promoted Met-tRNAf binding to 40S ribosomes depends absolutely on the presence of a polyribonucleotide messenger containing an initiation codon (such as AUG or GUG). Other polyribonucleotide messengers tested, such as poly(U), poly(A) and poly(A,C) were completely ineffective in this binding reaction. This result indicates that the Met-tRNAf.40S.mRNA complex is formed by a direct interaction between Met-tRNAf, 40S ribosomes and the initiation site in mRNA. A mechanism has been proposed for Met-tRNAf.40S.mRNA complex formation in yeast.

Heat-shock protein synthesis in Chlamydomonas reinhardi. Translational control at the level of initiation of a poly(A)-rich-RNA coded 22-KDa protein in a cell-free system

The effect of temperature on the in vitro translation of control and heat-shock poly(A)-rich RNA, obtained from Chlamydomonas reinhardi cells, incubated for 2 h at 25 degrees C respectively, was studied using the wheat-germ translation system. Incubation of the cells at 42 degrees C induces the synthesis of RNAs coding for several heat-shock proteins, including a 22-kDa major polypeptide as well as several proteins of 45-94 kDa, as demonstrated by run-off translation of polyribosomes isolated from intact cells. However, the high-molecular-mass heat-shock proteins are poorly translated in the wheat-germ system. The poly(A)-rich RNA coding for the 22-kDa heat-induced polypeptide has an apparent sedimentation coefficient higher than that expected from the molecular mass of its translation product, and was preferentially translated in vitro at temperatures above 31 degrees C as compared with pre-existing RNAs. Raising the temperature of translation, slightly inhibited (10%) the runoff translation of polyribosomes isolated from intact cells. However, when initiation was carried out in vitro for a short time at increasing temperatures and translation continued at 25 degrees C in the presence of aurintricarboxylic acid, the 22-kDa heat-shock polypeptides was preferentially translated. Aurintricarboxylic acid did not significantly inhibit incorporation of [35S]methionine when added to polyribosomes isolated from control or heat-shocked cells. From the above data we conclude that the translation of the 22-kDa heat-shock protein is controlled in vitro at the initiation level.

Initiation factors eIF4A and C1 from wheat germ and the formation of mRNA X ribosome complexes

The binding of ribosomes to mRNA is analyzed in a fractionated system from wheat germ with [3H]uridine-labeled poly(A)+ RNA prepared from germinating wheat embryos. The reaction requires factors eIF3, eIF4C, and eIF5; Met-tRNA and the Met-tRNA binding system; either GTP or GMP-PNP; ATP; and factors C1 and eIF4A. These requirements are identical to those previously found to be necessary for formation of ribosome X Met-tRNAMeti complexes, with the exception of ATP, and factors C1 and eIF4A. The function of factors C1 and eIF4A is therefore specifically related to the mRNA attachment reaction. The presence of GTP in the mRNA binding reaction results in the formation of 80 S ribosome complexes, while with GMP-PNP only 40 S ribosome complexes are formed. Ribosome binding to native reovirus RNA in the fractionated wheat germ system is similar to the reaction with poly(A)+ RNA, strongly requiring ATP and factors C1 and eIF4A. Binding to inosine-substituted reovirus RNA, however, is only partially dependent upon ATP, and both the ATP-dependent and the ATP-independent binding reactions strongly require factor C1 and are substantially stimulated by factor eIF4A. The ATP-independent reaction is inhibited by pm7GDP, has a strong requirement for Met-tRNAMeti, and the 40 S ribosome complex is stable to RNase. These results indicate that the ATP-independent binding of ribosomes to inosine-substituted reovirus RNA proceeds through the normal initiation process. They further suggest that neither factor C1 nor eIF4A function exclusively to unwind mRNA secondary structure. Since eIF4A is required for the ATP-independent binding to inosine mRNA, and at the same time interacts with ATP in the reaction with ATP-requiring mRNAs, this factor may have two roles in protein chain initiation, one related to the mRNA X ribosome interaction, and one related to the function of ATP.

Probing the function of the eucaryotic 5' cap structure by using a monoclonal antibody directed against cap-binding proteins

A monoclonal antibody directed against cap-binding proteins was used to elucidate the possible mechanism by which cap-binding proteins function in initiation of eucaryotic translation. The monoclonal antibody preparation employed in this study exhibited a marked differential effect in inhibiting the translation of folded, capped eucaryotic-mRNAs to a far greater extent than naturally uncapped mRNAs or native capped mRNAs that do not possess extensive 5' end secondary structure. These findings were consistent with the effects of the antibody on initiation complex formation with three different types of reovirus mRNA: native reovirus mRNA; inosine-substituted reovirus mRNA, which has a relaxed secondary structure; and bromouridine-substituted reovirus mRNA, in which base pairing is enhanced relative to regular reovirus mRNA. The extent that translation initiation complex formation was inhibited by the monoclonal antibody directly correlated to the degree of secondary structure present in the mRNA. Binding of bromouridine-substituted reovirus mRNA to ribosomes was inhibited to the greatest extent, while binding of inosine-substituted reovirus mRNA was not inhibited at all in the reticulocyte lysate system or was slightly inhibited in a wheat-germ system. These results support the hypothesis that cap-binding proteins are involved in unwinding of the 5' terminal, secondary structure of many eucaryotic mRNAs, thus facilitating the attachment of ribosomes to mRNA.

Characterization of an initiating cell-free protein synthesis system derived from rabbit brain

Protein synthesis in the brain is known to be affected by a wide range of treatments. The detailed analysis of the mechanisms that are involved would be facilitated by the development of cell-free translation systems derived from brain tissue. To date, brain cell-free systems have not been fully characterized to demonstrate a capacity for initiation of translation. The following criteria were utilized to demonstrate that a cell-free protein synthesis system derived from rabbit brain was capable of initiation in vitro: (a) sensitivity of cell-free translation to the initiation inhibitor aurintricarboxylic acid (ATA); (b) binding of [35S]Met-tRNAf to 40S and 80S initiation complexes; (c) incorporation of labeled initiation methionine into high-molecular-weight proteins; and (d) the association of labeled exogenous mRNA with polysomes. The optimum conditions for amino acid incorporation in this system were 4 mM-Mg2+, 140 mM-K+, and pH 7.55. Incorporation was dependent on the addition of ATP, GTP, and an energy-generating system. Cell-free protein synthesis reflected the normal process, since a similar spectrum of proteins was synthesized in vitro and in vivo. This initiating cell-free translation system should have wide application in the analysis of the mechanisms whereby various treatments affect protein synthesis in the brain.

Role of ATP in binding and migration of 40S ribosomal subunits

Two assays have been devised to demonstrate ATP-dependent migration of 40S ribosomal subunits on messenger RNA. The first is a two-step runoff assay. Reovirus mRNA was initially loaded with 40S subunits by incubation with wheat germ ribosomes in the presence of the antibiotic edeine. During the second phase of the incubation, in which further attachment of ribosomes was inhibited, the preformed complexes were shown to dissociate (presumably by runoff) only if ATP was included in the reaction. A more direct demonstration of ATP-dependent migration of 40S subunits was carried out using 3' end-labeled brome mosaic virus mRNA. In the presence of edeine and ATP, 40S ribosomal subunits were shown to advance all the way to the 3' end of the message, as shown by protection of the labeled 3'-proximal segment against nuclease digestion. Depletion of ATP by the addition of hexokinase prevented this migration. A variety of observations has raised the possibility that attachment of eucaryotic ribosomes to messenger RNA proceeds via a "scanning mechanism." The hypothesis is that a 40S subunit binds initially at or near the 5' terminus of the message and subsequently migrates toward the interior, stopping when it encounters the first AUG triplet. If migration of 40S subunits requires ATP, as the present studies suggest, the scanning mechanism predicts that in a system depleted of ATP a single 40S ribosome should be trapped near the 5' terminus of the message--upstream of the AUG initiator codon. This prediction was confirmed by analyzing binding of wheat germ ribosomes to a synthetic ribopolymer in which the 5'-proximal region (lacking AUG codons) and the AUG-containing segment near the 3' end of the molecule were differentially labeled.

Proximity of mRNA5'-region and 18S rRNA in eukaryotic initiation complexes

Messenger RNA was covalently linked to 18S ribosomal RNA in eukaryotic 40S and 80S initiation complexes by photoreaction with an RNA cross-linking agent, 4'-substituted psoralen. The sites of interaction of the mRNA capped 5'-region included some 3'-ends of 18S rRNA.

Messenger ribonucleoprotein particles in dry wheat and rye embryos : In vitro translation and size distribution

Extracts prepared from dry wheat (Triticum aestivum L.; var. Cama) and rye (Secale cereale L.; var. Celestijner) embryos exhibit relatively high endogenous messenger activities in an in vitro protein synthesizing system: up to 400 pmol leucine are incorporated per 50 μl reaction mixture; the messenger/ribosome ratio is estimated at about 0.03. Sucrose gradient analysis of the incubation mixture during cellfree protein synthesis shows a progressive in vitro polysome formation with the native endogenous mRNPs. The translation of these messengers, although dependent on initiation, follows linear kinetics. The native mRNP particles can be separated on sucrose gradients in 6 distinct size classes with sedimentation values varying from 25 S to 104 S. Their size is strongly reduced after deproteinization so that the naked mRNAs sediment in a range between 8 S and 35 S. The molecular weights of the proteins synthesized under direction of the native RNA particles range from 12,000 to 70,000 as estimated by polyacrylamide gel electrophoresis.

Nucleotide regulation of a eukaryotic protein synthesis initiation complex;

Formation of a ternary initiation complex containing Met-tRNAf, GTP and eukaryotic initiation factor 2, is the first step in sequential assembly of the initiation complex. The concentration of GTP required for half maximal formation of the ternary complex is 2.5 with 10(-6) M. GDP is a potent competitive inhibitor of ternary complex formation with Ki = 3.4 with 10(-7) M. The nucleotide binding site on eukaryotic initiation factor 2 demonstrates relative specificity for GDP with KD(GDP) = 3.0 with 10(-8) M; 100-fold higher concentrations of GTP than GDP are required for displacement of either [(3)H]GDP or [(3)h]gtp from the necleotide binding site. An ATP-dependent stimulation of ternary complex formation observed in partially purified initiation factor preparations is due to nucleoside diphosphate kinase (EC 2.7.4.6) which serves to remove inhibitory levels of GDP by phosphorylation with ATP. Since GTP is hydrolyzed to GDP during protein synthesis, this provides a mechanism by which the ATP:ADP ratio may regulate the rate of initiation of protein synthesis.

Aurintricarboxylic acid and initiation factors of wheat embryo

In extracts of wheat embryo, aurintricarboxylic acid inhibits attachment of ribosomes to messenger RNA and has little effect on aminoacyl transfer to peptide. This specificity of inhibition allows (i) the demonstration that the initial phase of amino acid incorporation dependent on RNA of tobacco mosaic virus involves an "initiation" reaction between ribosome and messenger RNA which requires two soluble factors, (ii) an assay facilitating purification of the initiation factors, and (iii) the demonstration that these factors are distinct from aminoacyl transfer enzymes.