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PubMed1997

Translation and replication properties of the human rhinovirus genome in vivo and in vitro.

The poor translation efficiency of genome-length human rhinovirus RNA in vitro using HeLa cell extract-supplemented rabbit reticulocyte lysate has hampered the study of rhinovirus IRES-mediated translation and polyprotein synthesis in a cell-free system. In contrast, the efficient in vitro translation characteristics of poliovirus RNAs have ultimately allowed the programming of cell-free coupled translation/replication extracts which are able to produce infectious poliovirus particles in vitro. A possible explanation for the decreased burst size observed during the course of a rhinovirus infection, compared to poliovirus infection, is reduced levels of polyprotein synthesis in vivo. In order to test this hypothesis and extend in vitro translation/replication technology to the study of human rhinoviruses, a chimeric cDNA construct was engineered which allowed the in vitro synthesis of T7 transcripts containing the intact poliovirus type 1 (PV1) 5' noncoding region (5' NCR) and initiation codon upstream of the human rhinovirus 14 (HRV14) polyprotein-coding region and 3'-terminal sequences. These chimeric RNAs translated efficiently in vitro and were used successfully to program a cell-free replication extract. Unexpectedly, parental HRV14 RNAs also translated efficiently in the HeLa cell-free translation/replication extract but replicated less efficiently than the chimera in vitro. The chimeric HRV14/PV1 RNAs were infectious and gave rise to a virus with a growth phenotype similar to that of parental HRV14. Preliminary characterization of this chimeric virus suggests that the biological properties characteristic of rhinovirus in vivo are determined primarily by the rhinovirus gene products. Although the translation efficiency of the HRV14 5' NCR may be a limitation in rabbit reticulocyte lysate-based in vitro translation extracts, it does not appear to be a major limiting determinant for growth of rhinovirus in vivo or replication in the HeLa cell-free extract.

Animals↗

PubMed1991

Characterization of mucin glycoprotein-specific translation products from swine and human trachea, pancreas and colon.

RNA was isolated from cultured swine trachea epithelial cells and mucus-secreting tumor cell lines from human pancreas, lung and colon by extraction with guanidine isothiocyanate. Poly(A)+mRNA rich fractions were purified by repeated chromatography on oligo (dT)-cellulose columns and they were translated in a cell-free rabbit reticulocyte system. Translation products labelled with 35S-methionine were isolated by immunoprecipitation with specific antibodies to the polypeptide chains of mucin glycoproteins and they were analyzed by SDS-PAGE and fluorography. A single principal polypeptide band of 67 kDa was found in all cases when the immunoprecipitates were washed with buffer containing bovine serum albumin and unlabeled deglycosylated mucin glycoprotein. The intensity of the 67 kDa band decreased when unlabeled deglycosylated mucin glycoprotein was added to the translation mixture before immunoprecipitation. Affinity purified monospecific antibodies elicited against chemically deglycosylated polypeptide chains of purified mucin glycoproteins from human and swine trachea and Cowper's gland were all equally effective in immunoprecipitating the 67 kDa translation product. Monospecific antibodies directed against the glycosylated and unglycosylated regions of the polypeptide chain yielded single bands with a molecular size of 67 kDa in each case. Peptide profiles obtained by digestion of the 67 kDa translation product with S. aureus V-8 protease were identical to those obtained with deglycosylated human and swine trachea mucin glycoproteins. These studies clearly demonstrate that the translation product of swine trachea and human lung, colon and pancreatic mucin glycoprotein gene is a single polypeptide chain of 67 kDa. The relative size and properties of the translation products synthesized with poly (A)+RNA isolated from mucus-secreting cells derived from three different tissues are similar to those of mucin glycoproteins purified directly from mucus secretions of human and swine trachea epithelium.

Animals↗

PubMed1980

Translational accuracy enhanced in vitro by (p)ppGpp.

The effect of (p)ppGpp on the accuracy of translation in vitro was studied with a system that has a missense error frequency similar to that of living bacteria. When poly (U) is translated, limitation of the system in Phe increases the Leu missense error frequency. The introduction of (p)ppGpp to the Phe-limited mixtures reduces significantly the missense errors as well as reduces the rate of translation. The introduction of (p)ppGpp to a full system has no effect on the accuracy of translation but does reduce its rate. The effects of (p)ppGpp on rate and accuracy of translation can be simulated in part by other inhibitors of translation such as GDPCP, fusidic acid and tetracycline. Furthermore, the presence of ppGpp or GDPCP in a Phe-limited system leads to an accumulation of Phe-tRNA, while a Phe-limited system that contains only GTP has negligibly small concentrations of Phe-tRNA. We conclude that one way in which (p)ppGpp improves the accuracy of translation is by permitting the system to maintain a favorable Phe-tRNA/Leu-tRNA ratio.

Cell-Free System↗

PubMed1987

The yeast nuclear gene CBS1 is required for translation of mitochondrial mRNAs bearing the cob 5' untranslated leader.

Mitochondrial translation of the cob mRNA to yield apocytochrome b is specifically dependent on the nuclear gene CBS1, while mitochondrial translation of the oxi2 mRNA to yield cytochrome oxidase subunit III (cox III) is specifically dependent on the nuclear gene PET494. Chimeric oxi2 mRNAs bearing the 5' leaders of other mitochondrial mRNAs, transcribed from rho- mitochondrial DNAs termed MSU494, are translated in pet494 mutants. In this study, we examined translation of coxIII from MSU494-encoded chimeric mRNAs in zygotes of defined nuclear and mitochondrial genotype. CoxIII was translated from a chimeric mRNA bearing the cob leader only when the zygotes contained a wild-type CBS1 gene. CoxIII translation from an mRNA bearing the 5' leader of the mitochondrial gene aap1 was not dependent on CBS1 activity. We conclude that the product of the nuclear gene CBS1, or something under its control, acts in the mitochondrion on the cob mRNA 5' leader to activate translation of down-stream coding sequences.

Cell Nucleus↗

PubMed1982

Translational attenuation of ermC: a deletion analysis.

ermC is a plasmid gene which specifies resistance to macrolide-lincosamide-streptogramin B antibiotics. The product of ermC was previously shown to be an inducible rRNA methylase, which is regulated translationally, and a mechanism for this regulation, termed the translational attenuation model, has been proposed. This model postulates that alternative inactive and active conformational states of the ermC mRNA are modulated by erythromycin-induced ribosome-stalling during translation of a leader peptide. In the present study the translational attenuation model was tested by constructing a series of deletants missing the ermC promoter and portions of the regulatory (leading) region. In these mutants, ermC transcription is dependent on fusion to an upstream promoter. Depending on the terminus of each deletion within the regulatory region, determined by DNA sequencing, ermC expression is observed to be either high level and inducible (like the wild-type), high level and noninducible, or low level and noninducible. The translational attenuation model predicts that as the deletions extend deeper into the leader region, successively masking and unmasking sequences required for translation of the methylase, an alternation of high and low level methylase expression will be observed. These predictions are confirmed. Based on this and other information, the model is refined and extended, and both direct translational activation and kinetic trapping of a metastable active intermediate during transcription are proposed to explain basal synthesis of methylase and to rationalize the effects of certain regulatory mutants.

Bacillus subtilis↗

PubMed1990

Translational coupling in the pyrF operon of Salmonella typhimurium.

The pyrF gene, encoding the sixth enzyme of pyrimidine biosynthesis in Salmonella typhirmurium, appears to be the first gene of an operon. The second gene, orfF, encodes a 11.5 kDa polypeptide of unknown function. To study the regulation of orfF expression directly, transcriptional and translational fusions of orfF to galK and lacZ, respectively, were constructed and the level of expression of the reporter genes was determined under different growth conditions. The results obtained show that the synthesis of OrfF and orotidine 5'-phosphate decarboxylase is coordinately controlled by pyrimidines, and that this control occurs at the level of transcription. The orfF translational start codon overlaps the pyrF translational stop codon, suggesting that the two genes are translationally coupled. This was investigated by studying how frameshift mutations, which cause premature termination of pyrF translation at different points, affect orfF expression. All mutations reduced orfF expression markedly without interfering with transcription of the gene. Thus, expression of pyrF and orfF are translationally coupled. Inspection of the nucleotide sequence of the pyrF/orfF junction region suggests that formation of secondary structures on the naked mRNA may explain the low level of orfF expression in the absence of translation of the pyrF terminal region.

Amino Acid Sequence↗

PubMed1990

Successful competition in translation by the flavivirus Kunjin with poliovirus during co-infections in Vero cells.

Infection with poliovirus effectively inhibited the translation of Vero cell messengers (carrying type 1 or type 2 caps at the 5' end) and of influenza virus messengers (type 1 caps) in co-infections. In contrast, Kunjin virus RNA (type 1 caps) and Semliki Forest virus RNA (a togavirus, with type 0 caps) continued to be translated in the presence of co-infecting poliovirus. Translation of Kunjin virus RNA was also unaffected during co-infections with either influenza virus or Semliki Forest virus. Guanidine treatment effectively blocked poliovirus replication only, but the inhibitory effect on translation of cell messengers and influenza virus messengers was still observed, indicating that this effect was not caused by competition in translation with poliovirus messengers. It was therefore concluded that the observed inhibition was most likely caused by cleavage of the p220 subunit of the cap binding protein (CBP) complex of the cell normally required for translation of capped messengers, as reported by others. However, Kunjin virus RNA could be efficiently translated apparently in the absence of a functional CBP complex, except when its secondary structure was stabilized by hypertonic salt in the culture medium.

Animals↗

PubMed1991

"In situ" translation: use of the cytoskeletal framework to direct cell-free protein synthesis.

We have developed a novel, "in situ" translation system derived from cultured cells that are subject to mild detergent extraction. By using a low concentration of nonionic detergent to gently permeabilize cells while they remain adherent to a substrate, cytoskeletal frameworks are obtained that are devoid of membraneous barriers yet retain much the same topological arrangement of mRNA, ribosomes and cytostructure that exists "in vivo". Data indicate that when these cytoskeletal frameworks are supported by a ribosome-depleted, nuclease-treated, reticulocyte lysate supernatant, they are capable of resuming translation of their attached polysomes for at least 40 minutes. Emulsion autoradiography of ongoing protein synthesis demonstrates that protein synthetic activity is ubiquitous throughout the population of extracted cells, and not confined to a less well-extracted subset. Computer-assisted, two-dimensional gel analysis reveals that the pattern of proteins produced by such extracted cells is approximately 70% coincident with that produced by unextracted cells, including proteins of molecular weight as great as 200 kilodaltons. Furthermore, a continued increase in intensity of almost all proteins during the first 40 minutes of translation suggests that translational re-initiation, in addition to polysome run-off, is also taking place. Collectively, these findings indicate that much of the translational machinery remains both intact and competent in this cytoskeletal-based translation system. As such, this system should prove extremely useful in identifying molecular factors operant during certain types of translation control and in further examining the role played by the cytoskeleton in regulating gene expression.

Animals↗

PubMed1985

Molecular assessment of S1 endonuclease-resistant snapback hairpin loops generated by DNA polymerase I during the in-vitro nick translation reaction.

The in-vitro nick translation reaction used to label DNA to high specific activity also produces aberrant DNA structures known as "snapback" hairpin loops. Hairpin structures are precluded from participating in precise DNA-DNA hybridization interactions. Three nick translation systems were all found to yield significant quantities of snapback hairpins, as determined by their resistance to S1 endonuclease digestion following denaturation. The relative quantities of hairpins produced correlated with both the mass average size of the final DNA probe product synthesized as well as the overall rate of the nick translation reaction. Decreases in the amount of exogenous DNase I used in nick translation reactions produced significant decreases in the amount of hairpin loop structures formed. Hairpins could be effectively removed from nick-translated DNAs by employing hydroxylapatite column chromatography. Strategies to reduce hairpin formation during nick translation and the removal of hairpins from nick-translated DNAs are presented.

DNA↗

PubMed2005

Perceiving a stable world during active rotational and translational head movements.

When a person moves through the world, the associated visual displacement of the environment in the opposite direction is not usually seen as external movement but rather as a changing view of a stable world. We measured the amount of visual motion that can be tolerated as compatible with the perception of moving within a stable world during active, sinusoidal, translational and rotational head movement. Head movements were monitored by means of a low-latency, mechanical head tracker and the information was used to update a helmet-mounted visual display. A variable gain was introduced between the head tracker and the display. Ten subjects adjusted this gain until the visual display appeared stable during sinusoidal yaw, pitch and roll head rotations and naso-occipital, inter-aural and dorso-ventral translations at 0.5 Hz. Each head movement was tested with movement either orthogonal to or parallel with gravity. A wide spread of gains was accepted as stable (0.8 to 1.4 for rotation and 1.1 to 1.8 for translation). The gain most likely to be perceived as stable was greater than that required by the geometry (1.2 for rotation; 1.4 for translation). For rotational motion, the mean gains were the same for all axes. For translation there was no effect of whether the movement was inter-aural (mean gain 1.6) or dorso-ventral (mean gain 1.5) and no effect of the relative orientation of the translation direction relative to gravity. However translation in the naso-occipital direction was associated with more closely veridical settings (mean gain 1.1) and narrower standard deviations than in other directions. These findings are discussed in terms of visual and non-visual contributions to the perception of an earth-stable environment during active head movement.

Adult↗

PubMed2001

Why are translationally sub-optimal synonymous codons used in Escherichia coli?

Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force, so there is a balance between mutation, selection, and drift; (2) at some sites there is no selection on codon usage, so some synonymous sites are unaffected by translational selection; and (3) translationally sub-optimal codons are favored by alternative selection pressures at certain synonymous sites. We find that when all the data is considered, model 1 is supported and both models 2 and 3 are rejected as sole explanations for the existence of translationally sub-optimal codons. However, we find evidence in favor of both models 2 and 3 when the data is partitioned between groups of amino acids and between regions of the genes. Thus, all three mechanisms appear to contribute to the existence of translationally sub-optimal codons in E. coli.

Codon↗

PubMed1999

A coding segment of the virulence regulatory gene spvR enhances expression of spvR-lacZ and spvR-gfp translational fusions in Salmonella typhimurium.

The Salmonella gene spvR is regulated by RpoS, and encodes an autoregulatory DNA-binding protein of the LysR family, which is required for transcriptional activation of the virulence operon spvABCD. We found that the 12-bp sequence between codons 3 and 8 of spvR (12bp-box) increased the expression of spvR'-lacZ translational fusions by at least two orders of magnitude. The 12bp-box did not affect the level of expression of a transcriptional spvR'-lacZ fusion, as determined by measurement of beta-galactosidase activity and mRNA levels. This suggests that the 12bp-box does not play a major role at the transcriptional level. However, the amounts of both SpvR-LacZ hybrid protein and lacZ mRNA produced from a translational spvR'-lacZ fusion were significantly lower if the 12bp-box was removed. Thus, the 12bp-box directly or indirectly affects the amount of spvR'-lacZ mRNA produced from a translational fusion but not from a transcriptional fusion. The 12bp-box still appeared to be functional when the spvR'-lacZ mRNA was elongated at its 5' end. In that case, however, while the 12bp-box greatly reduced the level of downstream mRNA produced, it did not affect the level of upstream mRNA. The effect of the 12bp-box was not restricted to lacZ fusions because expression of a translational spvR'-gfp fusion was also decreased by removal of the 12bp-box. The sequence of the 12bp-box is complementary to a sequence near the decoding region of 16S rRNA thought to be involved in translation initiation. This box may thus function as a translational enhancer, in which case the effect of the 12bp-box on lacZ mRNA levels might result indirectly from the tight coupling of translation and mRNA degradation. However, a direct role of the 12bp-box in increasing mRNA stability or in reducing the incidence of premature termination of transcription cannot be excluded.

Artificial Gene Fusion↗

PubMed1981

Further evidence for translational regulation of tyrosine aminotransferase synthesis by dibutyryl cyclic AMP in Reuber H35 hepatoma cells.

Cyclic AMP derivatives increase the rate of synthesis of tyrosine aminotransferase in Reuber H35 hepatoma cells. Various studies lend support to the hypothesis that cyclic AMP increases the synthesis of tyrosine aminotransferase by acting at a posttranscriptional site. The presence of a limited non-translatable pool of tyrosine aminotransferase mRNA prior to the formation of the translatable tyrosine aminotransferase mRNA implicates a possible site of action of cyclic AMP. We compared the capacity of N6,O2'-dibutyryl cyclic AMP to induce tyrosine aminotransferase synthesis when untranslatable tyrosine aminotransferase mRNA sequences are present or absent. The transition of a condition in which non-translatable tyrosine aminotransferase mRNA sequences were present to a condition in which they were absent was established by preinduction of Reuber H35 cells with dexamethasone, followed by addition of actinomycin D. In the time period thereafter, the amount of non-translatable mRNA decreased and 1.5-2 h after addition of actinomycin D, only translatable tyrosine aminotransferase mRNA was present. It can be seen that the induction of tyrosine aminotransferase synthesis by dibutyryl cyclic AMP follows the normal decrease of tyrosine aminotransferase mRNA. We present evidence that dibutyryl cyclic AMP in Reuber H35 hepatoma cells regulates tyrosine aminotransferase synthesis at a posttranscriptional site independent of the pool of non-translatable tyrosine aminotransferase mRNA sequences, but influencing the efficiency of translation of active tyrosine aminotransferase mRNA.

Animals↗

PubMed1991

Translational discrimination of ribosomal protein mRNAs in the early Drosophila embryo.

Most Drosophila mRNAs are actively translated in the early embryo, with the exception of the poorly translated ribosomal protein (r-protein) mRNAs. Two possible mechanisms for this translational discrimination were tested: (1) Translation of r-protein mRNAs is discriminated against by the limited activity of translational initiation factors in the early embryo and (2) translation of r-protein mRNAs is repressed by trans-acting factors that reversibly bind these mRNAs. Exogenously provided initiation factors promoted partial recruitment of r-protein mRNAs into polysomes, suggesting that modulation of initiation factor activity may play a role in the translational discrimination of r-protein mRNAs during embryogenesis. No evidence for involvement of reversibly binding trans-acting factors was obtained, although there are limitations in the interpretation of the latter experiments.

Actins↗

PubMed1992

Cell-free translation in reversed micelles.

Cell-free translation in reversed micelles (RM) of surfactants in organic solvents is demonstrated using as an example the synthesis of human interleukin-2 by the wheat germ translation system solubilized in Brij 96 (oleyl-poly(10)oxyethylene ether) RM in cyclohexane. The translation system components and the product were recovered from the RM system by acetone precipitation. The recovery and translation reaction yields depended on the degree of surfactant hydration. The translation yields in Brij 96 RM were close to that observed in regular aqueous solution. The Brij 96 RM system is regarded as a promising media for the cell-free synthesis of hydrophobic proteins. Meanwhile, no translation reaction was observed in Aerosol OT (sodium bis(2-ethylhexyl) sulfosuccinate) RM in octane, which presumably is due to the ability of Aerosol OT to bind Mg2+ ions necessary for the functioning of the translation apparatus.

Cell-Free System↗

PubMed1984

Interspersed poly(A) RNAs of amphibian oocytes are not translatable.

The poly(A) RNA of the Xenopus oocytes has been shown to include both single copy and interspersed transcripts. Interspersed maternal poly(A) RNAs contain repetitive sequence elements distributed within regions transcribed from single copy sequences. When renatured these RNAs form partially double-stranded RNA networks, and as shown earlier this can be utilized for preparative separation of interspersed maternal transcripts from maternal transcripts that remain single-stranded after renaturation (Anderson et al., 1982). The translational activity of these RNA fractions was tested in vitro, in wheat germ and reticulocyte systems. While the single-stranded fractions supported protein synthesis, the interspersed oocyte RNAs displayed little translational activity. Translational activity was measured in vivo by injection into the Xenopus oocyte. Oocytes previously injected with globin mRNA were injected with increasing amounts of single-stranded, double-stranded, or denatured double-stranded RNA fractions, and the amount of globin synthesis was determined. It was found that single-stranded RNA competes with globin mRNA for the limited translational apparatus of the oocyte, as manifested by a quantitative reduction of globin synthesis. However, globin synthesis was not affected when double-stranded RNA, either in renatured or denatured form, was injected. We conclude that the interspersed RNAs are not translated within the oocyte. The amount of single and double-stranded RNAs loaded onto polysomes in the injected oocytes was also determined. Sixty seven per cent of radio-iodinated single-stranded RNA pelleted with polysomes in injected oocytes, whereas less than 20% of similarly labeled double-stranded RNA pelleted with polysomes. This value is similar to that obtained when partially hydrolyzed RNA is injected, suggesting again that essentially none of the interspersed RNA is translated in vivo. The significance of these findings in relation to translational regulation during oogenesis and early development is discussed.

Animals↗

PubMed1986

Changes in the half-life of ribosomal protein messenger RNA caused by translational repression.

The half-life of ribosomal protein operon L11 mRNA in vivo was measured during exponential growth by following the kinetics of incorporation of radioactive precursors into L11 mRNA transcribed from multi-copy plasmids. The degree of translational feedback regulation by L1, the L11 operon-specific translational repressor protein, was changed by altering the site on the "L11 mRNA" where L1 interacts. The half-life of the overproduced L11 mRNA increased by about fivefold when translational repression was abolished, while the half-life of mRNA from the spc ribosomal protein operon, which is not translationally regulated by L1, stayed constant. Furthermore, the half-life of L11 operon mRNA carrying an additional mutation in the ribosome binding site that abolishes translation remains short. This indicates that the change in half-life observed during increased gene dosage is due to translational repression by L1 and is probably a consequence of L1 blocking translation of L11 mRNA and not due to some nucleolytic activity mediated by L1.

Base Sequence↗

PubMed1983

The effect of poliovirus infection on the translation in vitro of VSV messenger ribonucleoprotein particles.

Messenger ribonucleoprotein (mRNP) particles were isolated and examined for the presence of factors involved in the inhibition of protein synthesis induced by poliovirus infection. Vesicular stomatitis virus (VSV) mRNPs were used as a model for cellular mRNPs. These mRNPs were translated in HeLa cell extracts with a similar efficiency and optimal conditions to that of purified mRNA, but they were not translated in extracts prepared from poliovirus-infected HeLa cells, which have been shown to be defective in cap-binding protein activity. We conclude that mRNP proteins do not include cap-binding protein activity, since the mRNPs were not able to bypass the restriction on translation of capped mRNAs in polio-infected cell extracts. In addition, VSV mRNPs were isolated from polio-superinfected cells, in which their translation was inhibited. These mRNPs were translated in vitro as well as normal VSV mRNPs. No evidence of a modification or a blocking factor on the mRNPs which prevented their translation following polio infection was observed. Thus, within the limits of the in vitro translation assays used, no factors involved in the discrimination between polioviral and cellular or VSV mRNA could be detected in the mRNP particle.

Carrier Proteins↗