Recognition of messenger RNA in eukaryotic protein synthesis. Equilibrium studies of the interaction between messenger RNA and the initiation factor that binds methionyl-tRNAf

Studies on the posttranscriptional site of cAMP action in the regulation of the synthesis of tyrosine aminotransferase

Synthesis of L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) can be induced by N6,O2'-dibutyryl-adenosine 3',5'-monophosphate (Bt2cAMP) in Reuber H35 cell cultures. Actinomycin D fails to block this induction which indicates a target for Bt2cAMP at a posttranscriptional level. We have determined the influence of Bt2cAMP on several translational events during the tyrosine aminotransferase synthesis with the following results. (1) The number of nascent tyrosine aminotransferase chains increased, whereas no effect was measured on the number of nascent total protein chains. (2) The rate of elongation along the tyrosine aminotransferase mRNA and total mRNA is not enhanced by Bt2cAMP. (3) The induced synthesis of tyrosine aminotransferase is more sensitive to the inhibition of elongation. We conclude from our results that Bt2cAMP induces the synthesis of tyrosine aminotransferase by an increase in the rate of initiation on the tyrosine aminotransferase mRNA.

The RNA-binding properties of protein synthesis initiation factor eIF-2

Protein synthesis initiation factor eIF-2 bound ATP in the presence or absence of Mg2+ ions. ATP impaired the binding of GTP or GDP to eIF-2. However, excess GTP did not significantly decrease the binding of ATP to eIF-2, suggesting eIF-2 has distinct ATP and GTP binding sites. Highly purified eIF-2 can bind mRNA, and this did not require the mRNA to be capped. mRNA binding was saturable, and maximal binding corresponded to about 0.4 mol mRNA bound per mol eIF-2. GTP, and, at lower concentrations, GDP, inhibited the binding of mRNA to eIF-2. In addition, ATP and other nucleoside triphosphates decreased mRNA binding. The implications of these findings for the structure and function of eIF-2 are discussed. Preparations of eIF-2 deficient in the beta-subunit showed reduced ability to bind mRNA, suggesting that while it is not essential for mRNA binding, this subunit is involved in the interaction. Consistent with this is the observation that ultraviolet crosslinking of mRNA to eIF-2 resulted primarily in labelling of the beta-subunit. Subsequent analysis revealed that mRNA was cross-linked to the C-terminal region of eIF-2b which contains a putative Zn-finger structure.

Binding of eukaryotic initiation factor-2 and trans-acting factors to the 5' untranslated region of encephalomyocarditis virus RNA

The encephalomyocarditis virus 5' untranslated region (EMC 5' UTR) has a binding site for eukaryotic initiation factor eIF-2. Mutations in the 3' end or deletion of the 5' end of the internal ribosomal entry site had a negative effect on the binding of eIF-2 to the EMC 5' UTR. The binding of eIF-2 to the mutant 5' UTRs was completely inhibited by the addition of competitor tRNA. Cross-linking of the EMC 5' UTR with proteins from rabbit reticulocyte lysates showed binding of trans-acting factors p52 and p57. Deletions in the 5' end of the internal ribosomal entry site resulted in a loss of the ability to bind trans-acting factor p57, in accordance with literature data, while p52 binding to these deletion mutants was weak compared to the wildtype EMC 5' UTR. Mutations in the 3' part of the 5' UTR of EMC still resulted in binding of both trans-acting factors, as with wild type RNA, but binding was more sensitive to competitor tRNA when compared to the binding of p52/p57 to the wild type 5' UTR.

Brain non-adenylated mRNAs

Most eukaryotic messenger RNA (mRNA) species contain a 3'-poly(A) tract. The histone mRNAs are a notable exception although a subclass of histone-encoding mRNAs is polyadenylated. A class of mRNAs lacking a poly(A) tail would be expected to be less stable than poly(A)+ mRNAs and might, like the histones, have a half-life that varied in response to changes in the intracellular milieu. Brain mRNA exhibits an unusually high degree of sequence complexity; studies published ten years ago suggested that a large component of this complexity might be present in a poly(A)- mRNA population that was expressed postnatally. The question of the existence of a complex class of poly(A)- brain mRNAs is particularly tantalizing in light of the heterogeneity of brain cells and the possibility that the stability of these poly(A)- mRNAs might vary with changes in synaptic function, changing hormonal stimulation or with other modulations of neuronal function. The mRNA complexity analyses, although intriguing, did not prove the existence of the complex class of poly(A)- brain mRNAs. The observed mRNA complexity could have resulted from a variety of artifacts, discussed in more detail below. Several attempts have been made to clone members of this class of mRNA. This search for specific poly(A)- brain mRNAs has met with only limited success. Changes in mRNA polyadenylation state do occur in brain in response to specific physiologic stimuli; however, both the role of polyadenylation and de-adenylation in specific neuronal activities and the existence and significance of poly(A)- mRNAs in brain remain unclear.

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.

Distinct epitopes in eukaryotic initiation factor 2 for binding of mRNA and for ternary complex formation with methionyl-tRNA(f) and GTP

Eukaryotic initiation factor 2 (eIF-2) forms a ternary complex with methionyl-tRNA(fMet) and GTP on one hand, and it binds to a specific site in mRNA molecules on the other. Antibodies directed against eIF-2 were used to analyze these dual binding activities. A monoclonal antibody directed against the beta-subunit of eIF-2, 5A4, is able to inhibit ternary complex formation as well as binding of mRNA, showing that this subunit is essential for both binding activities of eIF-2. However, a polyclonal antibody, PR1, is able to distinguish between these activities in the eIF-2 molecule. In the presence of PR1, binding of mRNA by eIF-2 is inhibited completely, yet ternary complex formation with methionyl-tRNA(fMet) and GTP is stimulated more than 5-fold. Apparently, specific antibodies to eIF-2 can induce a conformational change in inactive factor molecules that permits them to form ternary complexes. These results show that distinct epitopes in eIF-2 are involved in binding of mRNA and in ternary complex formation with methionyl-tRNA(fMet) and GTP.

Relief of cytotoxicity and enhancement of interferon inducer activity of double-stranded RNA by eukaryotic initiation factor 2

Double-stranded RNA (dsRNA) is a powerful interferon inducer but also possesses toxic properties. dsRNA was shown previously to inhibit translation by causing the inactivation of eukaryotic initiation factor 2 (eIF-2) and to bind tightly to this protein. The cytotoxicity of dsRNA was analyzed simultaneously with the induction of interferon in murine fibroblast cultures. Incubation of dsRNA with eIF-2 leads to a significant reduction in toxicity, concomitant with a marked stimulation of interferon induction. The enhancement of dsRNA-dependent interferon induction by eIF-2 is sensitive to a monoclonal antibody directed against the beta-subunit of eIF-2. When injected in combination with dsRNA, eIF-2 potentiates the dsRNA-dependent survival of mice infected with a lethal dose of Mengo virus.

Initiation factor eIF2 associated with non-polysomal poly(A)-containing messenger ribonucleoproteins of cryptobiotic gastrulae of Artemia salina

Non-polysomal poly(A)-containing mRNP of A. salina cryptobiotic embryos is separated in mRNP active in protein synthesis and in repressed mRNP by sucrose gradient centrifugation. In the translationally active fraction the presence of eukaryotic initiation factor 2 (eIF2) is demonstrated by electroblotting of sodium dodecylsulphate/polyacrylamide gels on nitrocellulose and anti-eIF2 antibody detection. mRNP proteins with Mr of 40 000 and 42 000 are identified as the alpha and beta subunits of eIF2. The repressed mRNP is devoid of eIF2 and is associated with an inhibitor ribonucleoprotein composed of a small 85 +/- 2-nucleotide-long RNA and a protein with Mr of 64 000. The latter ribonucleoprotein is a potent inhibitor of the translationally active mRNP.

The nature of the interaction of eukaryotic initiation factor 2 with double-stranded RNA

In addition to binding messenger RNA molecules at specific sequences, eukaryotic initiation factor 2 (eIF-2) also binds to double-stranded RNA (dsRNA). The dsRNA is a powerful inhibitor of initiation of eukaryotic translation, causing the inactivation of eIF-2, but in the presence of certain mRNA templates, dsRNA fails to establish inhibition. Such mRNA templates bind to eIF-2 with higher affinity than does dsRNA, while globin mRNA, a template sensitive to inhibition, binds with lower affinity. Here, the nature of the interaction between dsRNA and eIF-2 was studied by examining both the binding of eIF-2 to Penicillium chrysogenum dsRNA molecules carrying 32P label at their 5' ends, and the ability of eIF-2 to protect such label against pancreatic ribonuclease digestion. The results reveal binding sites for eIF-2 at the 5' ends, as well as throughout internal regions of the dsRNA molecule. At least 15 molecules of eIF-2 can be accommodated on a 3000-base molecule of P. chrysogenum dsRNA. eIF-2 protects a 105-base-pair 5'-terminal fragment in dsRNA against digestion, but exhibits no noticeable preference for the 5' ends. By contrast, eIF-2 fails to protect label at the 5' ends of denatured dsRNA molecules, even though it binds to them at internal sites more avidly than to native dsRNA. Binding of eIF-2 to dsRNA is not restricted to specific sequences: eIF-2 binds with equal affinity to the synthetic dsRNA sequence, poly(rI . rC). The data support the interpretation that eIF-2 recognizes the A conformation in dsRNA rather than sequence. Apparently binding of eIF-2 at sites spaced 200 base pairs apart prevents relaxation of the intervening length of the double helix, thereby stabilizing the dsRNA molecule against ribonuclease attack. These results show that, even though dsRNA and mRNA compete in their binding to eIF-2, the structural features recognized by eIF-2 in these RNA species are distinct.

Ultraviolet-crosslinking reveals specific affinity of eukaryotic initiation factors for Semliki Forest virus mRNA

Eukaryotic initiation factors (eIF) associate readily with 32P-labeled Semliki Forest virus (SFV) mRNA in vitro, forming complexes which can be crosslinked by 254 nm ultraviolet irradiation. After ribonuclease digestion, the initiation factors were released and analysed by gel electrophoresis. Autoradiography revealed proteins by virtue of crosslinked 32P-labeled mRNA fragments. eIF-4A, -4B and -4C as well as three subunits of eIF-3 could be crosslinked with SFV mRNA. None of these proteins bound to ribosomal RNAs.

Isolation of a heme-controlled inhibitor of translation that blocks the interaction between messenger rna and eukaryotic initiation factor 2

A heme-controlled inhibitor of translation was isolated from the S-100 of rabbit reticulocytes by a novel procedure including chromatography on double-stranded ribonucleic acid (dsRNA)-cellulose. The inhibitor thus purified is extremely active and functionally resembles previously studied heme-controlled inhibitor preparations in terms of kinetics and extent of inhibition of translation, relief of inhibition by eukaryotic initiation factor 2 (eIF-2), relief of inhibition by 2-aminopurine, and preferential inhibition of alpha-over beta-globin synthesis. The action of this inhibitor on translation is resistant to treatment with bacterial alkaline phosphatase, micrococcal nuclease, or trypsin and to incubation at 95 degrees C, pH 2 or pH 12. The inhibitor not only is retained on DEAE-cellulose, phosphocellulose, and dsRNA-cellulose but also exhibits a high affinity for the dye Cibacron Blue, properties that suggest that it may be a protein. Unlike previously described heme-controlled inhibitor preparations, or preparations that did not pass over dsRNA-cellulose, the inhibitor recovered upon dsRNA-cellulose chromatography does not exhibit eIF-2 kinase activity. The inhibitor does not block ternary complex formation between eIF-2, methionyl-tRNAfMet, and GTP but inhibits the ability of eIF-2 to form a complex with labeled globin mRNA. In the presence of inhibitor, the formation of mRNA/eIF-2 complexes can be restored effectively by an excess of eIF-2 but not by an excess of mRNA. The inhibitor thus appears to block the interaction between eIF-2 and mRNA not by competing with eIF-2 for a binding site on mRNA but, instead, by acting on eIF-2 itself.(ABSTRACT TRUNCATED AT 250 WORDS)

Translational competition by mRNA species encoding albumin, ferritin, haemopexin and globin

Messenger RNA from rat liver was translated in a micrococcal-nuclease-treated reticulocyte lysate supplemented with liver tRNA. Synthesis of the liver proteins haemopexin, ferritin and albumin was analyzed by quantitative immunoprecipitation. The relative translation yield of these proteins changed as a function of the amount of mRNA present during protein synthesis, revealing the existence of translational competition between individual species of mRNA from the liver. The results show that the mRNA species encoding haemopexin, ferritin and albumin possess distinctly different abilities to compete for one or more critical components in translation, with competitive strength increasing in this order. Although on a weight basis total liver mRNA is apparently as effective a template for protein synthesis as is globin mRNA, the latter displays a greater resistance to inhibition of its translation by KCl. In analogy with the translation properties of alpha-globin and beta-globin mRNA [Di Segni, G., Rosen, H. and Kaempfer, R. (1979) Biochemistry, 18, 2847-2854], this finding suggests that globin mRNA possesses greater competitive strength than does total liver mRNA. Increasing amounts of globin mRNA competitively inhibit the translation of albumin and ferritin mRNA present in total liver mRNA. The competition is relieved by the addition of eukaryotic initiation factor eIF-2. Translation of ferritin mRNA responds more vigorously to relief by eIF-2 than does translation of albumin mRNA, a finding consistent with the observation that albumin mRNA competes more effectively than ferritin mRNA in translation. The results support the assumption that albumin mRNA possesses a greater affinity for eIF-2 than does ferritin mRNA.

Regulation of sea urchin glycoprotein mRNAs during embryonic development

Gastrulation in sea urchin embryos is accompanied by a striking increase in the synthesis of N-linked glycoproteins, and inhibitors of this process block gastrulation. In this report, the messages coding for N-glycosylatable proteins in the developing embryo of the sea urchin, Strongylocentrotus purpuratus, were examined. Total mRNA and mRNA isolated from membranes of the embryos at various stages of development were used to program a cell-free translation/glycosylation system prepared from rabbit reticulocyte lysate supplemented with dog pancreas microsomes. The glycosylated translation products were separated from the nonglycosylated products by concanavalin A-agarose and analyzed by gel electrophoresis. The results indicate that although the RNA derived from the membranes of gastrula-stage embryos contains messages coding for numerous glycoproteins, only trace amounts of glycoprotein messages are associated with membranes at earlier stages of development. mRNAs coding for four glycoproteins of M(r)s 70,000, 65,000, 51,000, and 30,000 were examined further in total RNA preparations from the developing embryo. The data indicate that the messages coding for the glycoproteins of M(r)s 65,000 and 51,000 are present also in the unfertilized egg and in the pregastrulation embryo. Because these two messages are not found associated with the membranes until gastrula stage, it is likely that the synthesis of these glycoproteins during gastrulation is regulated at the translational level. The messages coding for glycoproteins of M(r)s 70,000 and 30,000, on the other hand, are not detectable in the unfertilized egg and may be synthesized de novo by the embryos. Thus, the expression of these two glycoproteins during gastrulation is regulated at least in part on the transcriptional level. On the basis of these findings, it appears that different modes of regulation are used for different glycoproteins that are synthesized during gastrulation.

Positive and negative cAMP-mediated control of tyrosine aminotransferase synthesis in Reuber H35 hepatoma cells

Induction of L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) by N6,O2'-dibutyryl-adenosine 3',5'-monophosphate (Bt2cAMP) in Reuber H35 hepatoma cells reaches a maximum value between 3-5 h after addition of Bt2cAMP and subsequently decreases in the continuous presence of Bt2cAMP. We have investigated the kinetics of the increase, i.e. induction, and the decrease, i.e. the repressed state, of the tyrosine-aminotransferase-synthesizing system under these conditions. Our experimental results are as follows. 1. The repressed state of the tyrosine-aminotransferase-synthesizing system is not caused by a decrease in the intracellular cAMP concentration. 2. The repressed state is inhibited by actinomycin D (while induction is not inhibited). 3. During the repressed state no effect of dexamethasone on tyrosine aminotransferase synthesis is found, while during induction Bt2cAMP and dexamethasone act synergistically. 4. Longer starvation of the cells in serum-free medium has no influence on the kinetics of the induction/repressed state curve. From these results we have concluded that the mechanism of the transition to the repressed state of the tyrosine-aminotransferase-synthesizing system is essentially different from the mechanism of deinduction which occurs after removal of the inducer. Moreover, the repressed state of the system is a phenomenon which is induced by Bt2cAMP separately from induction at a different level of protein synthesis.

Genomic RNA of mengovirus V. Recognition of common features by ribosomes and eucaryotic initiation factor 2

Binding of ribosomes to the 32P-labeled genomic RNA of mengovirus was studied in lysates of mouse L929 and Krebs ascites cells under conditions for initiation of translation. Upon total digestion with RNase T1, the 32P-labeled RNA protected in either 40S or 80S initiation complexes yielded four unique, large oligonucleotides. Each of these oligonucleotides occurred once in the viral RNA molecule. The same four oligonucleotides were recovered from 80S initiation complexes formed in lysates in which unlabeled mengovirus RNA had been translated extensively, indicating that recognition by ribosomes was not modulated detectably by a viral translation product. The recognition of intact, 32P-labeled mengovirus RNA by eucaryotic initiation factor 2 (eIF-2) was examined by direct complex formation. Fingerprint analysis of the RNA protected by eIF-2 against RNase T1 digestion yielded three T1 oligonucleotides that were identical to three of the four oligonucleotides protected in either 40S or 80S initiation complexes. A physical map of the large T1 oligonucleotides of the mengovirus RNA molecule was constructed, and the four protected oligonucleotides were found to map internally, within the region between the polycytidylate tract and the 3' end. For either ribosomes or eIF-2, the protected oligonucleotides could not be arranged in a continuous sequence, suggesting that they constitute at least two widely separated domains. These results show that ribosomes recognize and blind to more than a single sequence in mengovirus RNA, located internally in regions that are far removed from the 5' end of the molecule. eIF-2 itself binds with high specificity to mengovirus RNA, recognizing apparently three of the four sequences recognized by ribosomes.

Specific binding of eukaryotic initiation factor 2 to satellite tobacco necrosis virus RNA at a 5'-terminal sequence comprising the ribosome binding site

The mRNA-binding property of eukaryotic initiation factor 2 (eIF-2) was examined by studying its interaction with satellite tobacco necrosis virus (STNV) RNA carrying a (32)P-labeled 5' end. The RNA molecules bound by limiting amounts of eIF-2 were isolated and digested with pancreatic and T1 RNases. Digestion patterns showed that the labeled STNV RNA preparation offered to eIF-2 was heterogeneous, containing more than 30 different 5' ends; by contrast, the RNA selected by eIF-2 possessed predominantly one 5' end, pApGpUp..., the 5'-terminal sequence of intact STNV RNA. Binding analysis of individual 5'-terminal fragments generated from isolated, intact, STNV RNA by partial digestion with T1 RNase showed that eIF-2 does not bind detectably to the 32-nucleotide fragment ending with the initiation codon AUG or to shorter ones, but it does bind the 44-nucleotide fragment that contains the ribosome binding site. In addition to the structural features localized at the 5' end of STNV RNA, eIF-2 appears to recognize a conformation found only in larger molecules, because intact RNA and large 5-'-terminal fragments are bound preferentially over smaller ones. However, binding of short 5'-terminal STNV RNA fragments to eIF-2 is specific, as judged by competition with STNV and ribosomal RNA. Finally, binding of eIF-2 to intact STNV RNA leads to a conformational change in the RNA that greatly facilitates cleavage by T1 and P1 RNases at sites in the vicinity of the initiation region. These results show that eIF-2 interacts specifically with the 5'-terminal region of STNV RNA that contains the ribosome binding site and causes local unfolding of the RNA structure.

Translational activity and functional stability of human fibroblast beta 1 and beta 2 interferon mRNAs lacking 3'-terminal RNA sequences

Polyadenylylated mRNA was purified from poly(I).poly(C)- and cycloheximide-superinduced human fibroblast (FS-4) cultures. The mRNA was subjected to electrophoresis through an agarose/CH3HgOH gel, and human fibroblast beta 1 and beta 2 interferon mRNAs were isolated. Each mRNA preparation was phosphorolyzed at 0 degrees C for 20 min by using a molar excess of polynucleotide phosphorylase to produce RNAs lacking poly(A) and then incubated at 37 degrees C for varying lengths of time to allow the phosphorylase to further digest the deadenylylated RNA from the 3' end in a processive and synchronous manner. Removal of the poly(A) (less than or equal to 100 residues) and approximately 100 adjacent residues from human fibroblast beta 1 interferon mRNA (native length, 900 residues, including a 3'-noncoding region of 203 residues) did not alter the translational activity or the functional stability of this mRNA in Xenopus oocytes, whereas deletion of the poly(A) and approximately 200 adjacent residues decreased its translational efficiency. On the other hand, removal of the poly(A) (approximately 200 residues) and approximately 200 adjacent residues from human fibroblast beta 2 interferon mRNA (native length, 1300 residues) did not alter the translational activity or the functional stability of this molecule in oocytes. Thus, neither the poly(A) nor large segments of the 3'-noncoding region (which includes the hexanucleotide A-A-U-A-A-A sequence, at least in the case of beta 1 mRNA) are required for the maintenance of the functional stability of human beta 1 and beta 2 interferon mRNAs in Xenopus oocytes.

Influence of mRNA secondary structure on binding and migration of 40S ribosomal subunits

Reovirus messenger RNA was modified by reaction with bisulfite (in denaturing conditions) or by incorporation of IMP in place of GMP, thereby irreversibly unfolding the mRNA. Messenger RNA in which the secondary structure was weakened or abolished retained the ability to bind to wheat germ ribosomes, suggesting that conformational features around the AUG codon are not required for ribosome recognition of mRNA. Ribosomes were not able to attach (directly) to spurious internal sites, even in extensively unfolded RNA, indicating that the monocistronic character of eucaryotic messages (in which initiation is limited to a single 5' proximal site) is not simply due to conformational masking of all the internal AUG codons. The secondary structure in eucaryotic messages does contribute to the fidelity of the translation process, however, because when 40S ribosomal subunits were incubated with denatured mRNA they failed to stop at the 5' proximal AUG codon. Extensive migration beyond the 5' region occurred when 40S ribosomes (in the absence of 60S subunits) attached to unfolded mRNA, implying that the secondary structure in native mRNA facilitates correct translation by impeding migration of 40S subunits beyond the 5' proximal initiation region. Secondary structure in mRNA may also modulate the efficiency of translation. Studies with BrUMP-substituted mRNA, in which the secondary structure is enhanced, suggested that the efficiency of mRNA binding to ribosomes decreases as the stability of the secondary structure increases.