Translational control by messenger RNA competition for eukaryotic initiation factor 2

PKR activation and eIF2α phosphorylation mediate human globin mRNA splicing at spliceosome assembly

Short elements in mammalian mRNA can control gene expression by activating the RNA-dependent protein kinase PKR that attenuates translation by phosphorylating cytoplasmic eukaryotic initiation factor 2α (eIF2α). We demonstrate a novel, positive role for PKR activation and eIF2α phosphorylation in human globin mRNA splicing. PKR localizes in splicing complexes and associates with splicing factor SC35. Splicing and early-stage spliceosome assembly on β-globin pre-mRNA depend strictly on activation of PKR by a codon-containing RNA fragment within exon 1 and on phosphorylation of nuclear eIF2α on Serine 51. Nonphosphorylatable mutant eIF2αS51A blocked β-globin mRNA splicing in cells and nuclear extract. Mutations of the β-globin RNA activator abrogated PKR activation and profoundly affected mRNA splicing efficiency. PKR depletion abrogated splicing and spliceosome assembly; recombinant PKR effectively restored splicing. Excision of the first intron of β-globin induces strand displacement within the RNA activator of PKR by a sequence from exon 2, a structural rearrangement that silences the ability of spliced β-globin mRNA to activate PKR. Thus, the ability to activate PKR is transient, serving solely to enable splicing. α-Globin pre-mRNA splicing is controlled likewise but positions of PKR activator and silencer are reversed, demonstrating evolutionary flexibility in how PKR activation regulates globin mRNA splicing through eIF2α phosphorylation.

Deciphering fact from artifact when using reporter assays to investigate the roles of host factors on L1 retrotransposition

Background

The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cancer, embryogenesis and neuronal development, it has become a priority to understand L1-host interactions and identify host factors required for its activity. Apropos to this, we recently reported that L1 retrotransposition in HeLa cells requires phosphorylation of the L1 protein ORF1p at motifs targeted by host cell proline-directed protein kinases (PDPKs), which include the family of mitogen-activated protein kinases (MAPKs). Using two engineered L1 reporter assays, we continued our investigation into the roles of MAPKs in L1 activity.

Results

We found that the MAPK p38δ phosphorylated ORF1p on three of its four PDPK motifs required for L1 activity. In addition, we found that a constitutively active p38δ mutant appeared to promote L1 retrotransposition in HeLa cells. However, despite the consistency of these findings with our earlier work, we identified some technical concerns regarding the experimental methodology. Specifically, we found that exogenous expression of p38δ appeared to affect at least one heterologous promoter in an engineered L1 reporter, as well as generate opposing effects on two different reporters. We also show that two commercially available non-targeting control (NTC) siRNAs elicit drastically different effects on the apparent retrotransposition reported by both L1 assays, which raises concerns about the use of NTCs as normalizing controls.

Conclusions

Engineered L1 reporter assays have been invaluable for determining the functions and critical residues of L1 open reading frames, as well as elucidating many aspects of L1 replication. However, our results suggest that caution is required when interpreting data obtained from L1 reporters used in conjunction with exogenous gene expression or siRNA.

Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells

BACKGROUND

The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translation. Here we address this issue by simultaneously profiling with microarrays the total mRNAs (the transcriptome) and the polysome-associated mRNAs (the translatome) after EGF treatment of human cells, and extending the analysis to other 19 different transcriptome/translatome comparisons in mammalian cells following different stimuli or undergoing cell programs.

RESULTS

Triggering of the EGF pathway results in an early induction of transcriptome and translatome changes, but 90% of the significant variation is limited to the translatome and the degree of concordant changes is less than 5%. The survey of other 19 different transcriptome/translatome comparisons shows that extensive uncoupling is a general rule, in terms of both RNA movements and inferred cell activities, with a strong tendency of translation-related genes to be controlled purely at the translational level. By different statistical approaches, we finally provide evidence of the lack of dependence between changes at the transcriptome and translatome levels.

CONCLUSIONS

We propose a model of diffused independency between variation in transcript abundances and variation in their engagement on polysomes, which implies the existence of specific mechanisms to couple these two ways of regulating gene expression.

Eukaryotic type translation initiation factor 2: structure-functional aspects

Translation initiation factor 2 (IF2) is one of key components of the translation initiation system in living cells. In bacteria IF2 is a multidomain monomeric protein, while in eukaryotic and archaean cells e/aIF2 is heterotrimer (αβγ). Data, including our own, on eukaryotic type translation initiation factor 2 (e/aIF2) structure and functioning are presented. There are also new data on initiation factors eIF5 and eIF2B that directly interact with eIF2 and control its participation in nucleotide exchange.

Connexin43 pseudogene in breast cancer cells offers a novel therapeutic target

Connexin43 (Cx43) is often deregulated in breast cancer tissue compared with normal adjacent tissue. Stable reexpression of Cx43 in cancer slows growth and renders the cells more sensitive to cytotoxic chemotherapeutics. Pseudogenes are often considered nonfunctional copies of DNA. The Cx43 pseudogene (PsiCx43) possesses all the features of an expressed gene and is exclusively transcribed in breast cancer cell lines and not in normal cells. PsiCx43 can be translated in vivo, and its protein exhibits growth-suppressive behavior similar to Cx43. We showed that PsiCx43 binds to the polyribosomes in breast cancer cells and that exogenous expression of PsiCx43 induces translational inhibition of Cx43. Furthermore, PsiCx43 is translated and binds more efficiently to the translational machinery than does Cx43 in an in vitro system. Following knockdown of PsiCx43 in breast cancer cells, we observed an increase in Cx43 RNA and protein. This results in increased cellular sensitivity to cytotoxic chemotherapy. Our results show that PsiCx43 acts as a posttranscriptional regulator of Cx43 in breast cancer cells, and that this represents an example of the regulation of genes by pseudogenes with potential therapeutic implications in cancer.

Human interferon-gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon-inducible protein kinase PKR

PKR, an interferon (IFN)-inducible protein kinase activated by double-stranded RNA, inhibits translation by phosphorylating the initiation factor eIF2alpha chain. We show that human IFN-gamma mRNA uses local activation of PKR in the cell to control its own translation yield. IFN-gamma mRNA activates PKR through a pseudoknot in its 5' untranslated region. Mutations that impair pseudoknot stability reduce the ability to activate PKR and strongly increase the translation efficiency of IFN-gamma mRNA. Nonphosphorylatable mutant eIF2alpha, knockout of PKR and PKR inhibitors 2-aminopurine, transdominant-negative PKR, or vaccinia E3L correspondingly enhances translation of IFN-gamma mRNA. The potential to form the pseudoknot is phylogenetically conserved. We propose that the RNA pseudoknot acts to adjust translation of IFN-gamma mRNA to the PKR level expressed in the cell.

Retroviral vectors for the expression of two genes in human multipotent neural precursors and their differentiated neuronal and glial progeny

Retroviral vectors allow stable integration of exogenous DNA into genomic DNA and therefore gene transmission to progeny. Multipotent neural precursors and immortal cell lines prepared from them have been demonstrated to integrate into either adult or developing brain in a nontumorigenic, functional manner, without interfering with normal neurobiological processes. These cells thus appear to provide a Trojan horse ideally adapted to directing the expression of transgenes appropriately in a host brain. Here we investigated and optimized the transduction capacity of MuLV-based retroviral vectors in which internal ribosomal entry segments (IRESs) drive coexpression of two heterologous gene products from a single bicistronic mRNA in a human multipotent neural precursor cell line, "Dev," which was prepared from a medulloblastoma. For this, two vectors containing two different combinations of three viral IRESs were used and the capacity of different pseudotyped vectors to permit an efficient and stable transduction of Dev cells was compared. Our data show that (1) the best recombinant vectors for Dev cell transduction are those pseudotyped with the 10A1 MuLV envelope (40% of transduction) and (2) the initial coexpression of neo and plap, observed in transduced undifferentiated Dev cells, is maintained in differentiated Dev cells with a neuronal or glial phenotype. Therefore, these double-IRES vectors may provide an efficient means of transducing the coexpression of two proteins in undifferentiated human neural precursors that is maintained in their differentiated progeny. These data suggest that the double-IRES strategy is well adapted to potential therapeutic situations when coexpression of two different transgenes may be required in the same cell.

Characterization of an internal ribosomal entry segment within the 5' leader of avian reticuloendotheliosis virus type A RNA and development of novel MLV-REV-based retroviral vectors

The murine leukemia virus (MLV)-related type C viruses constitute a major class of retroviruses that includes numerous endogenous and exogenous mammalian viruses and the related avian spleen necrosis virus (SNV). The MLV-related viruses possess a long and multifunctional 5' untranslated leader involved in key steps of the viral life cycle--splicing, translation, RNA dimerization, encapsidation, and reverse transcription. Recent studies have shown that the 5' leader of Friend murine leukemia virus and Moloney murine leukemia virus can direct cap independent translation of gag precursor proteins (Berlioz et al., 1995; Vagner et al., 1995b). These data, together with structural homology studies (Koning et al., 1992), prompted us to undertake a search for new internal ribosome entry segment (IRES) of retroviral origin. Here we describe an IRES element within the 5' leader of avian reticuloendotheliosis virus type A (REV-A) genomic RNA. Data show that the REV-A 5' IRES element maps downstream of the packaging/dimerization (E/DLS) sequence (Watanabe and Temin, 1982; Darlix et al., 1992) and the minimal IRES sequence appears to be within a 129 nt fragment (nucleotides 452-580) of the 5' leader, immediately upstream of the gag AUG codon. The REV-A IRES has been successfully utilized in the construction of novel high titer MLV-based retroviral vectors, containing one or more IRES elements of retroviral origin. These retroviral constructs, which represent a starting point for the design of novel vectors suitable for gene therapy, are also of interest as a model system of internal translation initiation and its possible regulation during development, cancer, or virus infection.

Translation of encephalomyocarditis virus RNA by internal ribosomal entry

Picornavirus 5' NCRs contain IRES elements that have been divided into two groups, exemplified by PV (type 1) and EMCV (type 2). These elements are functionally related and have an intriguing level of structural and sequence similarity. Some conserved RNA sequences and/or structures may correspond to cis-acting elements involved in IRES function, so that there may also be similarities in the mechanism by which the two types or IRES promote initiation. The function of both types of IRES element appears to depend on a cellular 57 kDa polypeptide, which has been identified as the predominantly nuclear hnRNP protein PTB. However, a specific function for p57/PTB in translation has not yet been established. These two groups can be differentiated on the basis of their requirements for trans-acting factors. The EMCV IRES functions efficiently in a broader range of eukaryotic cell types than type 1 IRES elements, probably because the latter require additional factor(s). A second distinction between these IRES element is that initiation occurs directly at the 3' border of type 2 IRES elements, whereas a nonessential spacer of between 30 nt and 154 nt separates type 1 IRES elements from the downstream initiation codon.

Initiation of protein synthesis in eukaryotes

The study of the regulation of initiation of protein synthesis has recently gained momentum because of the established relationship between translation initiation, cell growth and tumorigenesis. Therefore much effort is devoted to the role of protein kinases which are activated in signal transduction cascades and which are responsible for the phosphorylation of a number of initiation factors. These specific factors are mainly involved in the binding of messenger RNA to the 40S ribosome, a process that makes the unwinding of the 5' untranslated region necessary. It appears that the phosphorylation of these factors increases their ability for cap recognition and helicase activity. The enhanced phosphorylation of the messenger binding factors results not only in an overall stimulation of translation, but especially weak messengers are positively discriminated. The above mechanisms mainly deal with qualitative control of translation, i.e., messenger selection, but phosphorylation also plays a role in quantitative regulation of protein synthesis. The generation of active eIF-2, the initiation factor that binds the Met-tRNA(i) and GTP, is dependent on a factor involved in the GDP-GTP exchange. Phosphorylation of eIF-2 results in sequestration of the exchange factor and a slowing down of the rate of initiation.

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.

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.

Metabolism of host and viral mRNAs in frog virus 3-infected cells

Treatment of purified frog virus 3 (FV3) with nonionic detergent and high salt released an endoribonucleolytic activity and confirmed earlier findings of a virion-associated endonuclease. This observation, coupled with evidence implicating host and viral message destabilization in herpesvirus and poxvirus biogenesis, raised the question of what role, if any, mRNA degradation plays in FV3 replication. To answer this question, Northern analyses of mock- and virus-infected cells were performed using probes for representative host and viral messages. These studies demonstrated that the steady state level of host messages progressively declined during the course of productive FV3 infection, whereas the steady state level of viral messages was not affected. To determine whether the decline in the steady state level of host mRNA was due to virus-induced degradation or to normal turnover coupled to virus-mediated transcriptional shut-off, actin mRNA levels were examined in mock- and virus-infected cells in the presence and absence of actinomycin D. Under these conditions, actin mRNA levels declined more quickly in actinomycin D-treated, virus-infected cells, than in mock-infected cells incubated in the presence of actinomycin D suggesting that the decline in the steady state level of actin mRNA was due to degradation. However, although it appears as if host message degradation is responsible for virus-mediated translational shut-off, the ability of heat-inactivated FV3 to block cellular translation without destabilizing cellular messages indicates that message degradation is not required for translational inhibition. As noted above, the degradation of early FV3 messages was not involved in controlling the transition from early to late gene expression. Furthermore, the presence of abundant, but nontranslated, early messages late in infection, coupled with the inefficient translation of late messages in vitro supported earlier suggestions that FV3 gene expression is controlled, at least in part, at the translational level. Taken together, these results suggest that FV3 regulates gene expression in a unique manner and may be a good model to examine the mechanics of translational control.

An inhibitor(s) of globin mRNA translation in rabbit serum

1. A factor found in rabbit serum inhibits globin mRNA translation in vitro. 2. Inhibition of globin mRNA translation has been demonstrated in a cell-free rabbit reticulocyte lysate. 3. The inactivation of globin mRNA translation is not attributed to either serum albumin or ribonuclease activities. 4. Dialyzing the inhibitor for 24 hr at 4 degrees C does not result in the diminution of the inhibiting activity. However, the activity of the inhibitor is destroyed by heating to 70-80 degrees C for 5 min or by treatment with trypsin for 2 hr. 5. Ion exchange chromatography points to the inhibitor being a neutral protein, whereas, polyacrylamide gel electrophoresis reveals one major band with mol. wt 43 kDa. 6. The activity of the inhibiting material 3-fold greater in anemic serum than in normal serum. 7. These studies suggest that rabbit serum contains a protein inhibitor that may play a physiological role in regulating protein synthesis in red cells.

The 5'-untranslated region of picornaviral genomes

Picornaviruses are small naked icosahedral viruses with a single-stranded RNA genome of positive polarity. According to current taxonomy, the family includes four genera: Enterouirus (polioviruses, coxsackieviruses, echoviruses, and other enteroviruses), Rhinovirus, Curdiouirus [encephalomyocarditis virus (EMCV), mengovirus, Theiler's murine encephalomyelitis virus (TMEV)], and Aphthouirus [foot-and-mouth disease viruses (FMDV)]. There are also some, as yet, unclassified picornaviruses [e.g., hepatitis A virus (HAW] that should certainly be assessed as a separate genus. Studies on the molecular biology of picornaviruses might be divided into two periods: those before and after the first sequencing of the poliovirus genome. The 5'-untranslated region (5-UTR) of the viral genome was one of the unexpected problems. This segment proved to be immensely long: about 750 nucleotides or ∼10% of the genome length. There were also other unusual features (e.g., multiple AUG triplets preceding the single open reading frame (ORF) that encodes the viral polyprotein). This chapter shows that the picornaviral 5-UTRs are not only involved in such essential events as the synthesis of viral proteins and RNAs that could be expected to some extent, although some of the underlying mechanisms appeared to be quite a surprise, but also may determine diverse biological phenotypes from the plaque size or thermosensitivity of reproduction to attenuation of neurovirulence. Furthermore, a close inspection of the 5-UTR structure unravels certain hidden facets of the evolution of the picornaviral genome. Finally, the conclusions drawn from the experiments with the picornaviral5-UTRs provide important clues for understanding the functional capabilities of the eukaryotic ribosomes.

The alpha subunit of eucaryotic initiation factor 2 is phosphorylated in mengovirus-infected mouse L cells

Infection of mouse L cells with mengovirus resulted in the activation of a protein kinase (PK) that selectively phosphorylated the small, 38,000-molecular-weight alpha subunit of eucaryotic initiation factor 2 (eIF-2) in vitro. The mengovirus-activated kinase was detected in vitro approximately 3 h after virus adsorption. The ratio of phosphorylated to unphosphorylated eIF-2 also increased in vivo between 3 and 7 h after adsorption. The virus-activated kinase fractionated with the ribosomal pellet and had a high affinity for DEAE-cellulose and Mono Q ion-exchange columns. Gel electrophoresis of the kinase activity eluting from the Mono Q column and silver staining of the gel revealed only one protein band with a molecular mass of 70 kilodaltons. The optimal assay conditions for the mengovirus-activated kinase paralleled those of the double-stranded RNA-activated PK (dsRNA-PK). Lysates from infected cells contained elements capable of activating partially purified dsRNA-PK. These elements were identified as double-stranded RNA by their sensitivity to double-stranded RNase. The phosphorylation of the alpha subunit of eIF-2 coincided with the synthesis of dsRNA in infected cells, suggesting that the mengovirus-activated kinase is the dsRNA-PK. The phosphorylation of the alpha subunit of eIF-2 correlated with the global inhibition of protein synthesis that occurs at late times after infection.

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.

Frog virus 3-induced translational shut-off: activation of an eIF-2 kinase in virus-infected cells

Infection of susceptible fathead minnow or Friend erythroleukemia cells with either infectious or heat-inactivated frog virus 3 led to the rapid inhibition of cellular protein synthesis. As seen in other cells, translational shut-off was accompanied by the dissociation of polysomes, but not the degradation of irreversible inactivation of cellular mRNAs. In addition, lysates from cells infected with heat-inactivated FV3 showed a reduced capacity to synthesize protein and to form 43S pre-initiation complexes in vitro. These results indicate that the in vitro systems accurately reflected in vivo events, and suggest that translational shut-off occurred prior to the union of the 40S ribosomal subunit and the [eIF-2.GTP.Met tRNAi] ternary complex. To determine the basis for the translational block, lysates from mock- and FV3-infected cells were assayed in vitro for their ability to phosphorylate the alpha subunit of eIF-2. In contrast to lysates from mock-infected cells, lysates from cells infected with heat-inactivated or infectious FV3 readily phosphorylated the alpha subunit of eIF-2. Since phosphorylation of the alpha subunit of eIF-2 inhibits its catalytic utilization during polypeptide chain initiation, these findings suggest that translational shut-off mediated by FV3 may be due to activation of a kinase that selectively phosphorylates this key initiation factor.

Structure of the beta subunit of translational initiation factor eIF-2

A human liver cDNA encoding the beta subunit of protein synthesis initiation factor 2 (eIF-2) was isolated and sequenced. The 1416 bp cDNA encodes a protein of 333 amino acids (38,404 daltons) with characteristics that resemble authentic purified eIF-2 beta. De novo synthesized eIF-2 beta from cDNA transcripts incorporates into endogenous rabbit eIF-2 complexes. The protein possesses putative GTP-binding sites, a zinc finger motif, and a highly charged N-terminal region composed of three basic polylysine blocks separated by acidic domains. The polylysine blocks and the zinc finger motif suggest that eIF-2 beta interacts with RNA. A yeast protein, Sui3, isolated as an extragenic suppressor of his4 initiation codon mutations, exhibits extensive sequence identity with human eIF-2 beta, especially in the polylysine and zinc finger domains, thereby reinforcing the view that these elements are important for function.

Translational regulation of myelin basic protein synthesis

Synthesis of the mouse myelin basic proteins (MBPs) was studied in reticulocyte lysates programmed with brain mRNA in the presence or absence of brain factors. Addition of brain factors to the lysates increased the incorporation of [35S]methionine into total TCA-precipitable protein by a factor of 6-9, and the majority of this stimulation was found to be due to initiation factors. Although brain factors increased total protein synthesis, the percentage of MBP synthesis was reduced from 4.3% of the total counts incorporated (in the absence of brain factors) to 1.4% (in their presence). Increasing the concentration of brain mRNA in the lysates also reduced the relative levels of MBP synthesis. These results suggested the MBP mRNAs, as a group, were less efficiently initiated than most brain mRNAs. An analysis of the nucleotide sequence flanking the initiator codon of the MBP mRNAs indicates the presence of a second AUG codon 5 bases upstream, immediately followed by a termination codon, which may provide a structural explanation for the poorer initiation efficiency of the MBP mRNAs. Further analysis of the synthesis of the individual MBPs in the presence or absence of inhibitors of initiation (7-methylguanosine triphosphate and aurintricarboxylic acid) and elongation (anisomycin and emetine) indicated than the 14-kD MBP mRNA was less efficiently translated than the other MBP mRNAs. Synthesis of the 14-kD MBP was more strongly inhibited by the initiation inhibitors than the other MBP mRNAs, and synthesis of the 14-kD MBP was increased relative to the other MBPs in the presence of elongation inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of medium hypertonicity on reovirus translation rates. An application of kinetic modeling in vivo

Translation rates were determined for host and virus mRNAs in reovirus-infected SC-1 cells in hypertonic medium. The effect of low doses of cycloheximide on these translation rates was also measured. The results show that hypertonicity selectively stimulates viral translation relative to host translation. Moreover, in hypertonic medium, host translation is slightly stimulated by low doses of cycloheximide, whereas viral translation is markedly inhibited. This effect of cycloheximide is precisely the opposite to what was previously observed in isotonic media [Walden, W. E., Godefroy-Colburn, T., & Thach, R. E. (1981) J. Biol. Chem. 256, 11739-11746]. It is shown that both these effects of hypertonicity are predicted by the message competition/discrimination model previously described and thus provide support for the applicability of certain aspects of the model to translation rates in vivo.

Evidence for the presence of an inhibitor on ribosomes in mouse L cells infected with mengovirus

After infection of mouse L cells with mengovirus, there is a rapid inhibition of protein synthesis, a concurrent disaggregation of polysomes, and an accumulation of 80S ribosomes. These 80S ribosomes could not be chased back into polysomes under an elongation block. The infected-cell 80S-ribosome fraction contained twice as much initiator methionyl-tRNA and mRNA as the analogous fraction from uninfected cells. Since the proportion of 80S ribosomes that were resistant to pronase digestion also increased after infection, these data suggest that the accumulated 80S ribosomes may be in the form of initiation complexes. The specific protein synthetic activity of polysomal ribosomes also decreased with time of infection. However, the transit times in mock-infected and infected cells remained the same. Cell-free translation systems from infected cells reflected the decreased protein synthetic activity of intact cells. The addition of reticulocyte initiation factors to such systems failed to relieve the inhibition. Fractionation of the infected-cell lysate revealed that the ribosomes were the predominant target affected. Washing the infected-cell ribosomes with 0.5 M KCI restored their translational activity. In turn, the salt wash from infected-cell ribosomes inhibited translation in lysates from mock-infected cells. The inhibitor in the ribosomal salt wash was temperature sensitive and micrococcal nuclease resistant. A model is proposed wherein virus infection activates (or induces the synthesis of) an inhibitor that binds to ribosomes and stops translation after the formation of the 80S-ribosome initiation complex but before elongation. The presence of such an inhibitor on ribosomes could prevent them from being remobilized into polysomes in the presence of an inhibitor of polypeptide elongation.

The effect of serum deprivation on the initiation of protein synthesis in mouse neuroblastoma cells

Growth of mouse neuroblastoma cells becomes stationary when cultured in serum-free medium. Within 60 h, the protein-synthesizing capacity of the cells declines to 25% as compared to that of exponentially growing cells. The transitional activity of the crude ribosomal salt washes from serum-deprived and control cells was compared in in vitro protein-synthesizing pH 5 systems. It appears that the ribosomal salt wash from serum-deprived cells has significantly (70%) lost its ability to support the translation of neuroblastoma poly(A)+ RNA. This activity of the ribosomal wash from serum-deprived cells can be restored to control level with rabbit reticulocyte initiation factor eIF-4B only. The ability of the ribosomal wash from serum-deprived cells to support the translation of encephalomyocarditis virus (EMC) and Semliki Forest virus (SFV) 42 S mRNA was tested. We found that EMC-mRNA is efficiently translated with the ribosomal salt wash from serum-deprived cells, whereas on the other hand the translation of SFV 42 S mRNA is severely impaired. Therefore, we conclude that in serum-deprived neuroblastoma cells protein synthesis is regulated in both a quantitative and a qualitative way. Modulation of the activity of initiation factor of protein synthesis eIF-4B is at least partly responsible for the observed (selective) blockade of protein synthesis in serum-deprived cells.

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.

Cytoplasmic mRNA-protein complexes of chicken muscle cells and their role in protein synthesis

Irradiation of chicken muscle cells with ultraviolet light (254 nm) to cross-link RNA and protein moieties was used to examine the polypeptide complements of cytoplasmic mRNA-protein complexes (mRNP). The polypeptides of translationally active mRNP complexes released from polysomes were compared to the repressed nonpolysomal cytoplasmic (free) mRNP complexes. In general, all of the polypeptides present in free mRNPs were also found in the polysomal mRNPs. In contrast to polysomal mRNPS, polypeptides of Mr 28 000, 32 000, 46 000, 65 000 and 150 000 were either absent or present in relatively smaller quantities in free mRNP complexes. On the other hand, the relative proportion of polypeptides of Mr 130 000 and 43 000 was higher in free mRNPs than in polysomal mRNP complexes. To examine the role of cytoplasmic mRNP complexes in protein synthesis or mRNA metabolism, the changes in these complexes were studied following (a) inhibition of mRNA synthesis and (b) heat-shock treatment to alter the pattern of protein synthesis. Actinomycin D was used to inhibit mRNA synthesis in chick myotubes. The possibility of newly synthesized polypeptides of cytoplasmic mRNP complexes being assembled into these complexes in the absence of mRNA synthesis was examined. These studies showed that the polypeptides of both free and polysomal mRNP complexes can bind to pre-existing mRNAs, therefore suggesting that polypeptides of mRNP complexes can be exchanged with a pool of RNA-binding proteins. In free mRNP complexes, this exchange of polypeptides is significantly slower than in the polysomal mRNP complexes. Heat-shock treatment of chicken myotubes induces the synthesis of three polypeptides of Mr = 81 000, 65 000 and 25 000 (heat-shock polypeptides). Whether this altered pattern of protein synthesis following heat-shock treatment could affect the polypeptide composition of translationally active polysomal mRNPs was examined. The results of these studies show that, compared to normal cells, more newly synthesized polypeptides were assembled into polysomal mRNPs following heat-shock treatment. A [35S]methionine-labeled polypeptide of Mr = 80 000 was detected in mRNPs of heat-shocked cells, but not of normal cells. This polypeptide was, however, detected by AgNO3 staining of the unlabeled polypeptide of mRNP complexes of normal cells. These results, therefore, suggest that the assembly of newly synthesized 80 000-Mr polypeptide to polysomal mRNPs was enhanced following induction of new heat-shock mRNAs. The results of these studies reported here have been discussed in relation to the concept that free mRNP complexes are inefficiently translated in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)

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)

Regulation of heat-shock protein synthesis in chicken muscle culture during recovery from heat shock

Exposure of chick myotube cultures to a temperature (45 degrees C) higher than their normal growing temperature (37 degrees C) caused extensive synthesis of three major polypeptides of Mr = 25 000, 65 000 and 81 000 referred to as 'heat-shock polypeptides' (hsps). When these cells were allowed to recover from heat-shock treatment at 37 degrees C for 6-8 h, the rate of accumulation of isotope into the 65 000-Mr and 81 000-Mr hsps declined to levels comparable to those in control cultures maintained at 37 degrees C. However, incorporation of isotope in the 25 000-Mr hsp continued at an elevated rate for a longer period than the 65 000-Mr and 81 000-Mr hsps. When heat-shocked cells were allowed to recover at 37 degrees C in the presence of actinomycin D to block new mRNA synthesis, the hsp synthesis as measured by the incorporation of radioactive isotope in these polypeptides continued at levels comparable to those in heat-shocked cells prior to recovery. The block of recovery by actinomycin D was due to the presence of a greater amount of functional hsp mRNAs in the polysomes as compared to untreated controls. The role of competition between the mRNAs for hsps and normal cellular proteins for the translation machinery in regulating protein synthesis during the recovery from heat shock has been discussed.

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.

Protein synthesis in rat brain following neonatal exposure to lead

(1) Suckling rats were exposed to lead through the milk of their dams who received a diet of 4% lead carbonate and weanling rats were exposed to 2 injections of 5.0 mg Pb2+/100 g body weight. The brains were used to prepare the following homogenate fractions: postmitochondrial supernatant, postmicrosomal supernatant, ribosomes, initiation factors. (2) The postmitochondrial supernatant fractions were tested in vitro for protein synthesizing activity using the incorporation of labelled phenylalanine, and phenylalanyl-tRNA into peptide. The preparations from the lead-exposed rats had a significant reduction in activity. (3) Peptide formation with the brain ribosomes was not changed in the lead-exposed rats. (4) The aminoacyl-tRNA synthetase reaction was significantly reduced and accounted for most of the reduced peptide formation with brain homogenates from lead-exposed rats. (5) The binding of methionyl-tRNAfMet to ribosomes was increased using initiation factor preparations from the brain of lead-exposed rats.