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Results for “translational efficiency”

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PubMed2006

Correlation between translation efficiency and outcome of combination therapy in chronic hepatitis C genotype 3.

Combination therapy with interferon-alpha (IFN-alpha) and ribavirin (RBV) in chronic hepatitis C demonstrates the best responses against hepatitis C virus (HCV) of genotype 3. Still, it has proven to be ineffective in 20-30% of patients infected with this genotype. In the present study, we analysed the translation efficiency mediated by the internal ribosome entry site (IRES) region in HCV genotype 3 genomes isolated from sustained responders (SR) and non-responders (NR), assuming that this may influence the outcome of treatment. Pretreatment isolates of genotype 3 from 22 individuals (15 SR, seven NR) were selected for such analyses. The IRES region [nucleotide (nt) 1-407] was cloned into a dual luciferase vector and IRES activity assessed following transfection into various cell lines. Low relative translation efficiency was observed for IRES elements derived from SR patients, whereas those of NR patients showed significantly greater translation efficiency (29.7 +/- 13 vs 69.4 +/- 22; P < 0.01). Subsequently, the effect of IFN-alpha plus RBV on IRES-driven translation in vitro was determined. A greater suppressive effect was observed on IRES activity isolated from seven SR patients, when compared with seven NR patients. In conclusion, IRES efficiency in vitro correlated with treatment response for HCV genotype 3. Further studies are warranted to investigate whether IRES efficiency in vitro, or sequence motifs associated with IRES efficiency, will be worthwhile to explore as prognostic tools for other HCV genotypes in the treatment of chronic HCV infection.

Adult↗

PubMed1989

Influence of the 5'-end region of aldehyde dehydrogenase mRNA on translational efficiency. Potential secondary structure inhibition of translation in vitro.

mRNA coding for rat liver mitochondrial aldehyde dehydrogenase was translated in rabbit reticulocytes 10 times more efficiently than was the corresponding bovine mRNA. Previous data showed that the mRNAs primarily differed in the noncoding 5'-end (K.-L. Guan and H. Weiner, manuscript submitted for publication to Arch. Biochem. Biophys.). Fusion mRNAs were constructed so that the 5'-untranslated region from one was attached to the coding sequence of the other. Furthermore, the mRNAs were mutated at position -3, a position implicated in translational regulation, so that both contained the same residues. Results indicated that the dramatic difference in translational rates between rat and bovine mRNAs was just partly due to the sequence around the initiation codon. Secondary structure prediction of mRNA indicated that stable secondary structure could exist in the 5'-end of bovine mRNA, whereas no such stable structure should exist in rat mRNA. Existence of the predicted secondary structure of bovine mRNA was substantiated by the observation that termination in DNA sequencing in the 5'-end of bovine cDNA occurred. It is concluded that stable secondary structure in the 5'-end region of bovine mitochondrial aldehyde dehydrogenase performs a major role in inhibiting translation. This inhibitory effect is related to the magnitude of free energy required to melt the secondary structure in order to reach the initiation AUG codon.

Aldehyde Dehydrogenase↗

PubMed2002

A proinsulin gene splice variant with increased translation efficiency is expressed in human pancreatic islets.

As glucose-induced insulin expression is mainly regulated at the translational level, and such regulation often involves the 5'-untranslated region (5'UTR), we examined the human proinsulin gene 5'UTR. RT-PCR and sequencing demonstrated that a proinsulin splice variant (SPV) generated from a cryptic 5'-splice site and retaining the first 26 bp of intron 1 was present in human pancreatic islets from normal donors. The expression of this SPV was metabolically regulated, as shown by quantitative real-time RT-PCR, revealing a more than 10-fold increase in the SPV in isolated human islets incubated at 16.7 mM compared with 1.67 mM glucose. In vitro wheat-germ translation and in vivom transfection studies demonstrated that the altered 5'UTR of the SPV increased translation. The SPV yielded 4-fold more in vitro translated preproinsulin protein than the native proinsulin mRNA, and the SPV 5'UTR inserted upstream from a luciferase reporter gene resulted in a more than 6-fold higher luciferase activity, suggesting enhanced translation in vivo. Retention of the 26 bp changed the proposed secondary RNA structure of the SPV, which may facilitate ribosomal binding and explain the increase in translation efficiency. These results suggest a novel mechanism by which metabolic changes can modulate the expression of 5'UTR SPVs and thereby regulate translation efficiency.

5' Untranslated Regions↗

PubMed1992

Relationship between the 5'-leader sequence of mRNAs and the translation efficiency in a eukaryotic in vitro system.

To examine the effect of the 5'-leader region of mRNAs in regulating translation efficiency, chimeric mRNAs which have various sequences of the 5'-leader were synthesized by the SP6 in vitro transcription system, and translated in the wheat germ in vitro translation system. Translation efficiency was affected by the length of the 5'-leader and the number of the codon A-U-G at the translation initiation site.

Animals↗

PubMed1987

Differential translational efficiency of the mRNAs isolated from derepressed and glucose repressed Saccharomyces cerevisiae.

Carbon catabolite derepression induced changes in the pool of yeast mRNAs translatable in a protein-synthesizing reticulocyte system. Competition experiments with globin mRNA showed that the mRNA population obtained from derepressed cells possessed a higher translational efficiency than mRNA from repressed cells. The mRNAs that could account for the high translational efficiency of the derepressed mRNA were not detected in cells growing in glucose-rich medium. Analysis of protein synthesis in the presence of 7-methylguanosine 5'-phosphate indicated that the initiation factors recognizing the 5'-terminal structure of capped messengers interacted with lower affinity with the repressed than with some specific derepressed mRNAs.

Enzyme Repression↗

PubMed1989

Control of reovirus messenger RNA translation efficiency by the regions upstream of initiation codons.

The 10 species of reovirus messenger RNA are translated in vivo with efficiencies/frequencies that differ by as much as 100-fold. The s1 mRNA, which is translated 10 times less efficiently than the s4 mRNA but 10 times more efficiently than the/1 and m1 mRNAs, has a unique BamH1 cleavage site located immediately downstream of its initiation codon. Because the reovirus mRNAs have been cloned, this provides the opportunity for placing modified and altered sequences upstream of its coding sequence. The translation efficiencies of the variant mRNAs, transcribed via the SP6 in vitro transcription system, can then be measured in the rabbit reticulocyte lysate in vitro translation system. Using this system it was found that replacing the 5'-upstream sequence of the s1 mRNA with that of the s4 mRNA increases its in vitro translation efficiency by 4-fold; that the trinucleotide immediately upstream of the s1 initiation codon renders it very weak, and that it is only slightly superior to the weakest Kozak consensus sequence; that the nature of the nucleotides further upstream than position -3 can profoundly affect translation efficiency; that the nature of this effect is in turn markedly modified by the nature of nucleotides in positions -1 to -3; and that there is a minimum optimal 5'-upstream sequence length of about 14 nucleotides. We also investigated the effect of secondary structure involvement on the ability of 5'-upstream sequences to promote translation. Two effects were noted. First, being part of moderately stable stem loops (delta G, -18 kcal/mol) decreased translation efficiency about 3-fold; second, mRNA in which only three 5'-terminal nucleotides were unpaired were translated five times less efficiently than mRNA in which six nucleotides were unpaired. Accessibility of the 5'-cap as well as secondary structure of the 5'-upstream sequences are therefore factors that affect translation efficiency. Finally, we showed that the m1 mRNA, which is transcribed very poorly in vivo, is translated very efficiently in vitro; and that its 5'-upstream sequence is as effective in increasing protein sigma 1 formation as that of s4 mRNA. Since both m1 mRNA and protein mu 2 are stable in infected cells, the reason why m1 mRNA is translated so inefficiently in vivo therefore remains unexplained.

Codon↗

PubMed1985

Translation efficiency of zein mRNA is reduced by hybrid formation between the 5'- and 3'-untranslated region.

The secondary structure of zein mRNA affects its translation potential. Here we show that in a cell-free system the translation efficiency of zein mRNA containing inverted repeats in the 5'- and 3'-untranslated regions is reduced. This translational block is released after deletion of the 3'-inverted repeat. We conclude that the translational block is caused by hybrid formation between the two inverted repeats. The translational efficiency of zein mRNAs, is also affected by varying the length or the primary structure of the 5'-untranslated region.

3' Untranslated Regions↗

PubMed1989

Modulations of the in vitro translational efficiencies of Yellow Fever virus mRNAs: interactions between coding and noncoding regions.

As an approach to define the structural features within the 5' noncoding region of Yellow Fever virus (YFV) that modulate mRNA translational efficiency, we have studied how minor changes in this region affect the translational capacity in vitro of the corresponding mRNAs. A cDNA sequence coding for part of the YFV structural proteins was inserted into the vector pGEM3 containing the bacteriophage T7 promoter. This vector was engineered by site-directed mutagenesis to permit in vitro synthesis of transcripts containing only 5 vector nucleotides at their 5' end. The sequence of the YFV 5' untranslated region was further modified in order to alter the secondary structure of resulting T7 transcripts. The efficiency of these messengers in programming cell-free translation systems varied from 1- to 15-fold, correlating inversely with the potential of the 5' untranslated sequences to form stable secondary structures. A chimaeric messenger containing the YFV 5' noncoding (5' NC) region linked to a heterologous mRNA derived from Germiston virus, was tested for its in vitro translatability. We found a translational efficiency about 2-fold higher than that obtained with homologous transcripts, suggesting that YFV 5' NC region can function as a potential enhancer for gene expression. Data obtained with a series of plasmids constructed by linking the native YFV 5'NC region to various coding regions of the YFV genome indicated that interactions between the untranslated sequence and protein coding regions influence mRNAs translational efficiency.

Base Sequence↗

PubMed1998

Translational efficiency is up-regulated by alternative exon in murine IL-15 mRNA.

IL-15 promotes the growth of T cells and shares properties of IL-2. IL-2 is produced exclusively by T cells, while IL-15 message is expressed by a variety of tissues. However, it has been difficult to demonstrate IL-15 in the supernatants of many cells that express message for this cytokine. This suggests that IL-15 production is regulated by post-transcriptional controls. In this study, we cloned three types of murine IL-15 cDNA isoforms generated by alternative splicing and compared the translational efficiency among these isoforms. The translational efficiency of isoforms with alternative exon 5 containing another 3' splice site was significantly higher than that of IL-15 cDNA with originally described exon 5, which is generated by internal splicing of alternative exon 5. The translation product of the isoform containing alternative exon 5 has a shorter open reading frame due to stop codons in additional sequence, followed by a new AUG codon, and displays a shorter leader sequence. The shorter isoform of the IL-15 was detected in peritoneal macrophages stimulated with IFN-gamma and LPS, which expressed an abundant level of alternative exon 5. These results suggest that normal IL-15 production in stimulated macrophages is regulated by splicing of alternative exon 5.

Alternative Splicing↗

PubMed1981

Differential translation efficiency explains discoordinate expression of the galactose operon.

We have used an mRNA-dependent E. coli S-30 translation system to compare the translation efficiencies of two polycistronic transcripts of the galactose operon, the CRP-cAMP-dependent mRNA (P1) and the CRP-cAMP-independent mRNA (P2). The RNAs were prepared in vitro, quantitated by hybridization or gel analysis and translated in a cell free system. The specific protein products were measured, and their quantities were compared with the amount of input mRNA. Our results show that the P2 mRNA synthesizes epimerase, the 5'-proximal gene product of the gal operon, four times more efficiently than the P1 mRNA. The 5'-distal gene products, transferase and kinase, are translated with the same efficiency from both transcripts. Thus the ratio of epimerase to kinase synthesis is four times higher for the P2 mRNA than for the P1 mRNA. This change in epimerase to kinase ratio is identical to that observed in vivo when the cellular cAMP level falls and gal transcription is believed to switch from P1 to P2. We suggest that it is the differential translation efficiency of the epimerase gene on the two different gal transcripts that accounts for this discoordinate expression. Moreover, since the P2 mRNA differs from the P1 mRNA only by the addition of five nucleotides at the 5' terminus and these nucleotides are outside the ribosome binding region we determine for epimerase, the selective difference in the translation efficiency of epimerase is probably mediated by RNA conformation.

Carbohydrate Epimerases↗

PubMed1993

Translational regulation of human beta interferon mRNA: association of the 3' AU-rich sequence with the poly(A) tail reduces translation efficiency in vitro.

The 3' AU-rich region of human beta-1 interferon (hu-IFN beta) mRNA was found to act as a translational inhibitory element. The translational regulation of this 3' AU-rich sequence and the effect of its association with the poly(A) tail were studied in cell-free rabbit reticulocyte lysate. A poly(A)-rich hu-IFN beta mRNA (110 A residues) served as an inefficient template for protein synthesis. However, translational efficiency was considerably improved when the poly(A) tract was shortened (11 A residues) or when the 3' AU-rich sequence was deleted, indicating that interaction between these two regions was responsible for the reduced translation of the poly(A)-rich hu-IFN beta mRNA. Differences in translational efficiency of the various hu-IFN beta mRNAs correlated well with their polysomal distribution. The poly(A)-rich hu-IFN beta mRNA failed to form large polysomes, while its counterpart bearing a short poly(A) tail was recruited more efficiently into large polysomes. The AU-rich sequence-binding activity was reduced when the RNA probe contained both the 3' AU-rich sequence and long poly(A) tail, supporting a physical association between these two regions. Further evidence for this interaction was achieved by RNase H protection assay. We suggest that the 3' AU-rich sequence may regulate the translation of hu-IFN beta mRNA by interacting with the poly(A) tail.

Animals↗

PubMed1995

m7GpppG cap dependence for efficient translation of Drosophila 70-kDa heat-shock-protein (Hsp70) mRNA.

To investigate whether preferential translation of the heat-shock mRNAs occurs via cap-independent translation, the requirement for the m7GpppG cap structure for efficient translation of 70-kDa heat-shock-protein (Hsp70) mRNA was quantified by in vitro translation and by in vivo translation following electroporation. Hsp70 mRNA was transcribed in vitro with and without a cap structure. Translation in the rabbit reticulocyte or wheat germ lysate was reduced about 70% when the cap was absent. For comparison, translation of uncapped encephalomyocarditis virus 5'-untranslated-region-containing mRNA was equal to or greater than capped mRNA, whereas translation of several non-heat-shock mRNAs was reduced by 85-95% when capping was omitted. Cap-dependent translational stimulation of Hsp70 is not due to increased stability, is not a kinetic effect, and requires the methylated GpppG. To confirm the in vitro analyses, capped and uncapped mRNA were introduced into Drosophila tissue culture cells by electroporation, followed by heat shock. Paralleling the in vitro results, uncapped Hsp70 mRNA translation was 70-80% reduced relative to the capped form. Complementary experiments in which eIF-4 was inactivated in vitro using either m7GTP cap analogue or foot-and-mouth-disease virus L protease expression likewise indicated that the cap-dependent translation pathway is required for optimal Hsp mRNA translation. Since cellular Hsp70 mRNA translation during heat shock is very efficient, it is unlikely that translation via a cap-independent pathway is the principal basis for preferential translation.

Animals↗

PubMed1994

The role of the 3'-untranslated region of non-polyadenylated plant viral mRNAs in regulating translational efficiency.

Tobacco mosaic virus (TMV) is a positive-sense RNA virus in which the single genomic RNA functions as a messenger RNA. It is a member of a class of plant viral RNAs that are the only known non-polyadenylated mRNAs in plants. The 3'-untranslated region (UTR) of TMV genomic RNA is the functional equivalent of a poly(A) tail in that it increases mRNA stability and regulates translational efficiency. To determine whether the 3'-UTR of other non-polyadenylated plant viral mRNAs regulate translation, those from turnip yellow mosaic (TYMV), brome mosaic (BMV), and alfalfa mosaic (AlMV) viruses were investigated. Chimeric gene constructs were made in which the viral 3'-UTRs were introduced immediately downstream from the reporter genes encoding beta-glucuronidase (GUS) and luciferase (LUC), and were translated in plant protoplasts following delivery of the mRNA using electroporation. The 3'-UTR from BMV RNA3 regulated reporter gene expression in vivo to an extent comparable to that observed for the TMV 3'-UTR. The BMV 3'-UTR increased both message stability and translational efficiency. As regulators of translation, the BMV and TMV 3'-UTR were dependent on the presence of a cap at the 5' terminus for function. The 3' UTR of TYMV or AlMV RNA4 had little impact on translation or transcript stability. These data suggest that although the TMV 3'-UTR is not unique in regulating translation, the 3'-UTR of plant viral mRNAs do vary in their regulatory ability.

Base Sequence↗

PubMed1988

[Synthesis of visual rhodopsin in a cell-free translation system. I. Influence of the structure of the synthetic bovine visual opsin mRNA on its translational efficiency].

Influence of structural changes in nontranslated regions and translation initiation site of the in vitro synthesized bovine opsin mRNA on its translational efficiency in the wheat germ cell-free system has been studied. It is shown that level of the opsin synthesis up to 30 micrograms per 1 ml of translational mixture can be attained by optimizing structure of 5'-nontranslated region.

Animals↗

PubMed1986

Enhancement of translational efficiency by the Escherichia coli atpE translational initiation region: its fusion with two human genes.

The cDNA sequences encoding mature human interleukin 2 (IL2) and beta-interferon (INF beta), respectively, were fused with various translational initiation regions and inserted into two different types of expression vector. The relative levels of expression of the two genes and the functional stability of their respective mRNAs were examined in vivo in Escherichia coli hosts. The addition of the 30-bp sequence, found immediately upstream of the E. coli atpE gene Shine-Dalgarno (SD) sequence, to the translational initiation regions of IL2 and INF beta increased the expression of both these genes by a factor of 6-10. Thus this sequence, which naturally acts within the E. coli atp operon to enhance the translational initiation frequency of the atpE gene, can increase the expression of other genes in E. coli. It may exemplify a specific type of recognition signal for the E. coli translational apparatus.

Base Sequence↗

PubMed1990

A polymorphism affecting apolipoprotein A-II translational efficiency determines high density lipoprotein size and composition.

High density lipoproteins (HDL) are heterogeneous particles consisting of about equal amounts of lipid and protein that are thought to mediate the transport of cholesterol from peripheral tissues to liver. We show that a previously identified polymorphism affecting HDL electrophoretic mobility in mice is due to a monogenic variation controlling HDL size and apolipoprotein composition. Thus, the HDL particles of various inbred strains of mice exhibit a striking difference in the ratio fo the two major apolipoproteins of HDL, apoA-I and apoA-II. HDL particles in all strains examined contain an average of about five apoA-I molecules; however, whereas the strains with small HDL contain two to three apoA-II molecules per particle, the strains with large HDL contain about five apoA-II molecules per particle. This increase in the protein content of the large HDL is also accompanied by increased lipid content. The HDL size polymorphism and apoA-II levels cosegregate with the apoA-II structural gene on mouse chromosome 1, indicating that a mutation of the apoA-II gene locus is responsible. The rates of synthesis of apoA-II are increased in the strains with large HDL and high apoA-II levels as compared to the strains with small HDL and low apoA-II levels. On the other hand, the fractional catabolic rates of both apoA-I and apoA-II among the strains are very similar, confirming that apoA-II concentrations are controlled at the level of synthesis. Despite the difference in rates of apoA-II synthesis between strains, the apoA-II mRNA levels in the strains are not discernibly different, suggesting that a mutation of the apoA-II structural gene controls apoA-II translational efficiency. This was confirmed by translating apoA-II mRNA in vitro using a rabbit reticulocyte lysate system. Sequencing of apoA-II cDNA from the strains revealed a number of nucleotide substitutions, which may affect translational efficiency. We conclude that the assembly of apoA-II into HDL does not have a set stoichiometry but, rather, is controlled by the production of apoA-II. As apoA-II levels increase, the HDL particles become larger and acquire more lipid, but apoA-I content per particle remains unchanged. These studies with mice provide a model for the metabolic relationships between apoA-I, apoA-II, and HDL lipid in humans.

Amino Acid Sequence↗

PubMed1994

Correlation of translation efficiency with the decay of lacZ mRNA in Escherichia coli.

We isolated mutations in the leader of a ribosomal protein (r-protein)/lacZ fusion gene in Escherichia coli that caused the mRNA to be translated at efficiencies between < 1% and 62% of the rate of wild-type message. Using a subset of these mutants with translation efficiencies between 5% and 62%, we studied both physical and functional decay of the mRNA after rifampicin inhibition of transcription initiation. The decay of physically intact transcript was analyzed by gel electrophoresis of hybrid-selected messenger RNA segments. The output from the message was analyzed by measuring the synthesis rate of r-protein/lacZ fusion protein. Decay of physically intact message after rifampicin addition correlated with the translation efficiency, with the more active messengers being more stable. Different segments of the r-protein/lacZ fusion mRNA decayed with the same rate, indicating that there is no hyper-labile region in the transcript. The decay rate was also independent of the length of the segment probed, suggesting that the mRNA is not degraded by random attacks along the entire length of the molecule. Our results are consistent with an overall 5' to 3' degradation pathway. Surprisingly, the rate of fusion protein synthesis did not decrease immediately after rifampicin addition. Rather, a lag preceded the exponential decay phase; the length of this delay correlated with the translation efficiency, such that the lag increased with increasing efficiency of translation. We suggest that these lags indicate that mRNAs are normally competing for ribosomes during exponential growth and, after rifampicin addition, RNA molecules with longer physical half-lives are translated by ribosomes released from fast decaying messengers.

Base Sequence↗

PubMed1983

Regulation of ferritin mRNA: a possible gene-sparing phenomenon. Induction of ferritin synthesis by iron in liver as well as red cells combines high translational efficiency with increased utilization of preformed ferritin mRNA.

Control of ferritin synthesis by iron at the level of transcription is potentially hazardous to DNA because of the iron-catalyzed degradation of DNA. The induction of ferritin synthesis in reticulocytes of embryos (bullfrog tadpoles) occurs by two types of translational control i.e. increased availability of stored ferritin mRNA, in response to iron, coupled with a high translational efficiency. Since erythroid cell nuclei have large amounts of heterochromatin and may be relatively inactive genetically, the translational control of ferritin by iron observed in red cells was studied in other tissue by isolating poly (A+) RNA from tadpole liver and analyzing protein synthesis in vitro. Liver ferritin mRNA directed the synthesis of 7.0% of the protein in a wheat germ system, compared to 1.2% in vivo, suggesting that tadpole liver contained a large amount of stored ferritin mRNA. At levels of poly (A+) RNA which were saturating for total protein synthesis, ferritin synthesis was still linearly dependent upon RNA concentration, indicating a high efficiency of translation of ferritin mRNA. The results are analogous to those previously observed in red cells and confirm the storage of ferritin mRNA deduced from studies of the polysomal and nonpolysomal distribution of the mRNA in rat liver. The results indicate that the increased availability for translation of stored ferritin mRNA, in response to iron, and the high translational efficiency of ferritin mRNA are a general characteristic of ferritin synthesis rather than a specific feature of red cell maturation. This novel form of regulation of ferritin gene expression can be attributed to a need to protect DNA from degradation by iron and oxygen. The normal barrier between DNA and iron is apparently breached by the iron-oxygen complex of the drug bleomycin, an antitumor agent thought to act in vivo by iron-catalyzed cleavage of DNA.

Animals↗