The role of mRNA competition in regulating translation. II. Development of a quantitative in vitro assay

Amino acids Thr56 and Thr58 are not essential for elongation factor 2 function in yeast

Yeast elongation factor 2 is an essential protein that contains two highly conserved threonine residues, T56 and T58, that could potentially be phosphorylated by the Rck2 kinase in response to environmental stress. The importance of residues T56 and T58 for elongation factor 2 function in yeast was studied using site directed mutagenesis and functional complementation. Mutations T56D, T56G, T56K, T56N and T56V resulted in nonfunctional elongation factor 2 whereas mutated factor carrying point mutations T56M, T56C, T56S, T58S and T58V was functional. Expression of mutants T56C, T56S and T58S was associated with reduced growth rate. The double mutants T56M/T58W and T56M/T58V were also functional but the latter mutant caused increased cell death and considerably reduced growth rate. The results suggest that the physiological role of T56 and T58 as phosphorylation targets is of little importance in yeast under standard growth conditions. Yeast cells expressing mutants T56C and T56S were less able to cope with environmental stress induced by increased growth temperatures. Similarly, cells expressing mutants T56M and T56M/T58W were less capable of adapting to increased osmolarity whereas cells expressing mutant T58V behaved normally. All mutants tested were retained their ability to bind to ribosomes in vivo. However, mutants T56D, T56G and T56K were under-represented on the ribosome, suggesting that these nonfunctional forms of elongation factor 2 were less capable of competing with wild-type elongation factor 2 in ribosome binding. The presence of nonfunctional but ribosome binding forms of elongation factor 2 did not affect the growth rate of yeast cells also expressing wild-type elongation factor 2.

Use of Reticulocyte Lysates for Mechanistic Studies of Eukaryotic Translation Initiation

This chapter describes how commercially available, nuclease-treated rabbit reticulocyte lysates can be used to study different types of translation initiation (cap-dependent initiation, reinitiation, internal ribosome entry site-mediated initiation) and the influence of different initiation factors on these translation mechanisms. Additionally, with the use of sucrose gradients, it is possible to use nuclease-treated reticulocyte lysates to monitor the formation of ribosomal complexes for their content of mRNA, initiator met-tRNA(i), and initiation factors. The advantage of using nuclease-treated lysates rather than purified initiation factors is that reactions occur at or near the in vivo rate in contrast to rates observed in reactions with purified components, which are generally 10- to 1000-fold lower. The disadvantage is not being able to accurately control the amount of individual initiation factors, although the use of either factor additions or specific inhibitors can be helpful in assessing the role of specific individual initiation factors.

Translational regulation of rotavirus gene expression

Rotavirus mRNAs are transcribed from 11 genomic dsRNA segments within a subviral particle. The mRNAs are extruded into the cytoplasm where they serve as mRNA for protein synthesis and as templates for packaging and replication into dsRNA. The molecular steps in the replication pathway that regulate the levels of viral gene expression are not well defined. We have investigated potential mechanisms of regulation of rotavirus gene expression by functional evaluation of two differentially expressed viral mRNAs. NSP1 (gene 5) and VP6 (gene 6) are expressed early in infection, and VP6 is expressed in excess over NSP1. We formulated the hypothesis that the amounts of NSP1 and VP6 were regulated by the translational efficiencies of the respective mRNAs. We measured the levels of gene 5 and gene 6 mRNA and showed that they were not significantly different, and protein analysis indicated no difference in stability of NSP1 compared with VP6. Polyribosome analysis showed that the majority of gene 6 mRNA was present on large polysomes. In contrast, sedimentation of more than half of the gene 5 mRNA was subpolysomal. The change in distribution of gene 5 mRNA in polyribosome gradients in response to treatment with low concentrations of cycloheximide suggested that gene 5 is a poor translation initiation template compared with gene 6 mRNA. These data define a regulatory mechanism for the difference in amounts of VP6 and NSP1 and provide evidence for post-transcriptional control of rotavirus gene expression mediated by the translational efficiency of individual viral mRNAs.

NMDA receptor-mediated control of protein synthesis at developing synapses

We demonstrate a rapid and complex effect of N-methyl-d-aspartate receptor (NMDAR) activation on synaptic protein synthesis in the superior colliculi of young rats. Within minutes of receptor activation, translation of alpha Ca2+/calmodulin dependent kinase II (alphaCamK II) was increased, whereas total protein synthesis was reduced. NMDAR activation also increased phosphorylation of eukaryotic elongation factor 2 (eEF2), a process known to inhibit protein translation by reducing peptide chain elongation. Low doses of cycloheximide, which reduce elongation rate independently of eEF2 phosphorylation, decreased overall protein synthesis but increased alphaCaMK II synthesis. These observations suggest that regulation of peptide elongation via eEF2 phosphorylation can link NMDAR activation to local increases in the synthesis of specific proteins during activity-dependent synaptic change.

Differential roles of the 5' untranslated regions of cucumber mosaic virus RNAs 1, 2, 3 and 4 in translational competition

RNA species of plant tripartite RNA viruses show distinct translational activities in vitro when the viral RNA concentration is high. However, it is not known what causes the differential translation of virion RNAs. Using an in vitro wheat germ translation system, we investigated the translation efficiencies and competitive activities of chimeric cucumber mosaic virus (CMV) RNAs that contained viral untranslated regions (UTRs) and a luciferase-coding sequence. The chimeric RNAs exhibited distinct translation efficiencies and competitive activities. For example, the translation of chimeric CMV RNA 4 was about 40-fold higher than that of chimeric CMV RNA 3 in a competitive environment. The distinct translation resulted mainly from differences in competitive activities rather than translation efficiencies of the chimeric RNAs. The differential competitive activities were specified by viral 5 UTRs, but not by 3 UTRs or viral proteins. The competitive translational activities of the 5 UTRs were as follows: RNA 4 (coat protein)>RNAs 2 and 1 (2a and 1a protein, or replicase )> RNA 3 (3a protein).

A single-stranded loop in the 5' untranslated region of cucumber mosaic virus RNA 4 contributes to competitive translational activity

The 5' untranslated region (UTR) of cucumber mosaic virus (CMV) RNA 4 confers a highly competitive translational advantage on a heterologous luciferase open reading frame. Here we investigated whether secondary structure in the 5' UTR contributes to this translational advantage. Stabilization of the 5' UTR RNA secondary structure inhibited competitive translational activity. Alteration of a potential single-stranded loop to a stem by substitution mutations greatly inhibited the competitive translational activity. Tobacco plants infected with wild type virus showed a 2.5-fold higher accumulation of maximal coat protein than did plants infected with a loop-mutant virus. Amplification of viral RNA in these plants could not explain the difference in accumulation of coat protein. Phylogenetic comparison showed that potential single-stranded loops of 12-23 nucleotides in length exist widely in subgroups of CMV.

The 5' untranslated region of cucumber mosaic virus RNA4 confers highly competitive activity on heterologous luciferase mRNA in cell-free translation

The cell-free translation of virion RNAs of several tripartite RNA viruses has shown that RNA4, a subgenomic RNA, is more competitive than other virion RNAs. Recently, the 3' untranslated region (UTR) of alfalfa mosaic virus (AMV) RNA4 was identified to be a competitive determinant. In this study, we observed that the RNA4 of cucumber mosaic virus (CMV), another tripartite RNA virus, was also found to be a strong competitor in translational competition among CMV virion RNAs. To identify the competitive determinant of CMV RNA4, we constructed various chimeric luciferase mRNAs containing RNA4 and/or vector-derived UTRs. The relative translations of luciferase-containing mRNA in the presence of a competitor mRNA showed that the 5' UTR, not the 3' UTR, substantially contributed to the highly competitive activity of CMV RNA4.

Preferential translation of reovirus mRNA by a sigma3-dependent mechanism

We have characterized reovirus strains that differ in the degree to which they inhibit cellular protein synthesis and used them to investigate mechanisms regulating gene expression in infected cells. A previous genetic study associated distinct effects of reovirus strains on cellular translation with polymorphisms in viral protein sigma3. In cell extracts, sigma3 sequesters double-stranded RNA (dsRNA) and blocks activation of the dsRNA-activated protein kinase (PKR), an interferon-induced enzyme that inhibits translational initiation by phosphorylating elF-2alpha. We found that in infected cells, cellular protein synthesis is translationally regulated in a strain-specific manner. Using immunoprecipitation and indirect immunofluorescence we showed that the effect of a strain on cellular translation is not determined by the level of sigma3, but appears to result from differences in sigma3 localization. In cells infected with a strain that spares cellular translation, sigma3 is present throughout the cytoplasm, whereas in cells infected with inhibitory strains, sigma3 is restricted to perinuclear viral factories. Biochemical studies suggested that diffuse localization of sigma3 is a consequence of low affinity for capsid protein mu1. Our findings are consistent with a model in which the efficiency of cellular translation is determined by the cytoplasmic level of sigma3 that is not complexed with mu1.

Interaction of initiation factors with the cap structure of chimaeric mRNA containing the 5'-untranslated regions of Semliki Forest virus RNA is related to translational efficiency

Chimaeric chloramphenicol acetyltransferase (CAT) mRNA, containing the leader sequences of genomic 42S RNA and subgenomic 26S RNA of Semliki Forest virus (SFV) were synthesized by in-vitro transcription. These transcripts were translated with different efficiencies, as the authentic mRNA in SFV-infected cells. Therefore, they can be used as model mRNA species to study the mechanism underlying SFV-directed shut off of host protein synthesis. The interaction of translation initiation factors with the 5' cap structure was studied. Transcripts prepared in vitro using T7 RNA polymerase were capped and methylated posttranscriptionally with [32P]-GTP and S-adenosyl-L-methionine to yield cap-labelled mRNA species. Irradiation with ultraviolet light of 26S CAT and 42S CAT transcripts, together with crude rabbit reticulocyte initiation factors, resulted in the cap-specific cross-linking of eukaryotic initiation factors (eIF) eIF-4E and eIF-4B. The relative binding efficiency of these two factors to the cap structure of the various transcripts was, however, markedly different; the cap structure present in 26S CAT mRNA interacted efficiently with cap-binding proteins, whereas the cap structure of 42S CAT mRNA hardly bound to these proteins. Comparable results were obtained under competitive conditions. Data are presented that the secondary structure close to the 5' cap structure determines the efficiency of recognition of the mRNA by these initiation factors. Using a chemical cross-linking assay, it was demonstrated that eIF-4F, and also eIF-4E, differentially interacted with the cap structure of the various transcripts. The data are discussed with respect to the possible mechanisms involved in SFV-induced shut off of host cell protein synthesis.

Regulation of protein synthesis at the elongation stage. New insights into the control of gene expression in eukaryotes

There are many reports which demonstrate that the rate of protein biosynthesis at the elongation stage is actively regulated in eukaryotic cells. Possible physiological roles for this type of regulation are: the coordination of translation of mRNA with different initiation rate constants; regulation of transition between different physiological states of a cell, such as transition between stages of the cell cycle; and in general, any situation where the maintenance of a particular physiological state is dependent on continuous protein synthesis. A number of covalent modifications of elongation factors offer potential mechanisms for such regulation. Among the various modifications of elongation factors, phosphorylation of eEF-2 by the specific Ca2+calmodulin-dependent eEF-2 kinase is the best studied and perhaps the most important mechanism of regulation of elongation rate. Since this phosphorylation is strictly Ca(2+)-dependent, and makes eEF-2 inactive in translation, this mechanism could explain how changes in the intracellular free Ca2+ concentration may regulate elongation rate. We also discuss some recent findings concerning elongation factors, such as the discovery of developmental stage-specific elongation factors and the regulated binding of eEF-1 alpha to cytoskeletal elements. Together, these observations underline the importance of the elongation stage of translation in the regulation of the cellular processes essential for normal cell life.

Dissociation of double-stranded polynucleotide helical structures by eukaryotic initiation factors, as revealed by a novel assay

A new technique has been applied to the study of the RNA secondary structure unwinding activity of the eukaryotic initiation factors (eIFs) 4F, 4A, and 4B. Secondary structures were generated at the 5' ends of reovirus and globin mRNA molecules by hybridization with 32P-labeled cDNA molecules 15 nucleotide residues long. The dissociation of the labeled cDNAs from the mRNAs was assayed by a gel filtration chromatography procedure which separates the free cDNAs from mRNAs and mRNA/cDNA hybrids. When the three factors were tested alone, only eIF-4F stimulated dissociation of hybrids. The combination of eIF-4A plus eIF-4B also exhibited a strong hybrid dissociating activity, which was markedly temperature dependent. Under optimum conditions, up to 90% of the hybrid structures are disrupted in 60 min. These results demonstrate for the first time that stable double-stranded regions can be melted and dissociated by eIFs. They also characterize more precisely the first step in the structure unwinding reaction.

Modification of membrane permeability by animal viruses

Animal viruses modify membrane permeability during lytic infection. There is a co-entry of macromolecules and virion particules during virus penetration and a drastic change in transport and membrane permeability at the late stages of the lytic cycle. Both events are of importance to understand different molecular aspects of viral infection, as virus entry into the cell and the interference of virus infection with cellular metabolism. Other methods of cell permeabilization of potential relevance to understand the mechanism of viral damage of the membrane are also discussed.

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)

The three influenza virus polymerase (P) proteins not associated with viral nucleocapsids in the infected cell are in the form of a complex

The three influenza virus polymerase, or P, proteins (PB1, PB2, and PA) that are associated with viral nucleocapsids and are responsible for viral mRNA synthesis are in the form of a complex that moves down the template in association with the growing mRNAs during transcription (J. Braam, I. Ulmanen, and R.M. Krug, Cell 34:609-618, 1983). We determined whether infected cells contained a pool of P proteins not associated with viral nucleocapsids and, if so, whether the P proteins in this pool were in the form of a complex with each other. The cytoplasmic and nuclear extracts from infected cells were depleted of nucleocapsids by centrifugation, and the resulting supernatants were subjected to immunoprecipitation with an antiserum specific for either the PB1 protein or the PB2 protein. Both antisera precipitated all three P proteins, indicating that the P proteins were in a complex that was largely resistant to disruption by the detergents present in the immunoprecipitation buffer. Sucrose density gradient analysis showed that the P protein complexes ranged from about 11S to 22S and that almost all of the PB1 and PB2 protein molecules synthesized during a 1-h period (2.5 to 3.5 h postinfection) were in these complexes. Little or no free PB1 or PB2 protein was detected. The possible role of these nonnucleocapsid P protein complexes in the initiation and reinitiation of virus-specific RNA synthesis is discussed.

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.

Translational discrimination between the four RNAs of alfalfa mosaic virus. A quantitative evaluation

In an attempt to relate the translational characteristics of alfalfa mosaic virus (A1MV) RNAs to their structure [Ravelonandro et al. (1983) Nucleic Acids Res. 11, 2815-2826; Gehrke et al. (1983) Biochemistry 22, 5157-5164] we measured the relative affinities (discrimination ratios) of these RNAs for the initiation complex, in the wheat germ extract and in the nuclease-treated reticulocyte lysate, using a competition method designed by Brendler et al. [(1981) J. Biol. Chem. 256, 11747-11754]. As a prerequisite of this study we ascertained that the molecular mass distribution of the translation products was independent of RNA concentration in both translation systems. In the wheat germ extract the discrimination ratios are very similar for two strains of A1MV (S and B) which differ mainly by the presence (strain S) or absence (strain B) of a stable 5'-proximal hairpin. Hence this structure has no bearing on discrimination. Taking the affinity of RNA 3 as reference, the following orders of magnitude are found for the affinities of the different RNAs in the wheat germ: RNA 3, 1.0; RNA 1, 10; RNA 2, 60; RNA 4, 150. In the reticulocyte lysate the discrimination ratios are not significantly different from the wheat germ. Thus it seems that the mechanism of discrimination is essentially the same in the two translation systems, despite a difference in rate-limitation.

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.

Translation of vaccinia virus and cellular mRNA in cell-free systems prepared from uninfected and vaccinia virus infected L929 cells

Cell-free translation systems were prepared from uninfected and vaccinia infected (3 and 5 hours post-infection) L929 cells. The systems were made mRNA dependent in order to translate exogenous mRNA mixtures. The overall rate of protein synthesis was similar in the three translation systems. However, one-dimensional electrophoresis showed that the systems differed in terms of the translation efficiency for individual mRNAs. This could be demonstrated with each of the following mRNA mixtures: early vaccinia mRNA synthesized by vaccinia cores in vitro, mRNA isolated from polysomes of vaccinia infected HeLa cells ("late" vaccinia mRNA) and cytoplasmic ascites mRNA. When the above mentioned groups of mRNAs were allowed to compete for translation in the cell-free systems and their products were analyzed on one-dimensional gels, the following order of translational efficiency was observed: the most prominent species of vaccinia early mRNA (other species could not be judged) were translated better than some late vaccinia mRNA species which in turn were slightly more efficiently translated than cellular mRNAs.