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PubMed1997

Translation-competent extracts from Saccharomyces cerevisiae: effects of L-A RNA, 5' cap, and 3' poly(A) tail on translational efficiency of mRNAs.

Yeast genetics has proven fruitful in the identification of key players that are involved in translational initiation. However, the exact roles of many translation initiation factors in translation initiation remain unknown. This has been due to lack of a suitable in vitro translation system in which the mode of action of certain translation factors can be studied. This report describes the preparation of cell-free Saccharomyces cerevisiae lysates that can mediate the translation of exogenously added mRNAs. Optimal translation required the absence of viral L-A RNA in the lysate and the presence of both a 5' cap and a 3' poly(A) tail on the mRNAs. A cooperative effect of cap and poly(A) tail on translation initiation was observed, a property that has been found to operate in intact yeast cells as well. In addition, the yeast lysates mediated translational initiation through several viral internal ribosome entry sites, demonstrating that the yeast translation apparatus can perform internal initiation. Thus, these lysates may be useful in the biochemical analysis of cap-dependent and cap-independent translation events.

Protein Biosynthesis↗
PubMed1981

Preproceruloplasmin is a primary product of cell-free translation of ceruloplasmin messenger RNA.

Biosynthesis of ceruloplasmin was studied in wheat germ extract programmed with polysomal RNA from rat liver. Optimal potassium concentration for the total protein-synthesizing activity and for the synthesis of immunoreactive ceruloplasmin was 96 and 186 mM respectively. 7-methylguanosine 5'-monophosphate caused two-fold inhibition of the cell-free synthesis of ceruloplasmin. Immunoprecipitated ceruloplasmin that was synthesized at optimal potassium concentration was a homogeneous polypeptide of a molecular weight about 84 kD. The addition of membrane fractions from rat liver to the incubation mixture caused the conversion of the 84 kD polypeptide into 80 kD and 65 kD polypeptides that are similar to proceruloplasmins synthesized in rat liver during in vivo pulse labelling. The suggestion is made that 84 kD polypeptide is a primary product of the translation of ceruloplasmin mRNA (preproceruloplasmin).

Amino Acids↗
PubMed1980

In vitro synthesis of beta- and gamma-isoactins by messenger RNA of rat ascites hepatoma.

Messenger RNA was extracted from polysomes of rat ascites hepatoma, AH 7974, which contains both beta- and gamma-actins, and was translated in nuclease-treated reticulocyte lysate. The isoactins, beta and gamma, synthesized in vitro were characterized by (1) a high affinity to DNAase I-agarose; (2) polymerization with actin purified from bovine brain; (3) coelectrophoresis with bovine brain actin on two-dimensional gel, and (4) peptide mapping of each isoactin by partial digestion with papain (EC 3.4.22.2) followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The optimum conditions with respect to the concentration of RNA, Mg2+, and K+ for the synthesis of beta- and gamma-isoactins were identical: 300 micrograms/ml, 1.5 mM, and 100 mM, respectively. Aurintricarboxylic acid and 7-methyl-GMP (7MeGMP) inhibited the synthesis of beta- and gamma-actins to the same extent. These results strongly suggest that there is very little possibility of differential translational control of each isoactin gene. When polysomal RNA was separated by sucrose gradient centrifugation, both beta- and gamma-actin mRNAs appeared as a sharp peak at the region slightly heavier than 18 S RNA.

Actins↗
PubMed1992

Methylated cap structures in eukaryotic RNAs: structure, synthesis and functions.

There are more than twenty capped small nuclear RNAs characterized in eukaryotic cells. All the capped RNAs appear to be involved in the processing of other nuclear premessenger or preribosomal RNAs. These RNAs contain either trimethylguanosine (TMG) cap structure or methylated gamma phosphate (Mppp) cap structure. The TMG capped RNAs are capped with M7G during transcription by RNA polymerase II and trimethylated further post-transcriptionally. The Mppp-capped RNAs are transcribed by RNA polymerase III and also capped post-transcriptionally. The cap structures improve the stability of the RNAs and in some cases TMG cap is required for transport of the ribonucleoproteins from cytoplasm to the nucleus. Where tested, the cap structures were not essential for their function in processing other RNAs.

Animals↗
PubMed1989

Requirements for efficient in vitro transcription and translation: a study using yeast invertase as a probe.

Factors for efficient synthesis of mRNA in vitro and its subsequent translation in cell free lysates from reticulocyte and wheat germ were studied using yeast invertase as a probe. Among various transcription systems tested, containing either SP6, T5, T7 or a bacterial synthetic consensus promoter, the T7 system was superior both from a quantitative and qualitative point of view. Transcription with SP6 polymerase, but not with the other enzymes, resulted in premature transcript termination, which is ascribed to a sensitivity of the SP6 polymerase towards a hairpin loop structure in the invertase coding region. In-frame fusion of the critical DNA sequence to a different gene promoted premature transcription termination of the resulting chimeric template, which in its original form is transcribed correctly. Transcripts with additional sequences 5' upstream of the natural translation start revealed a diminished protein synthesis presumably due to the presence of out of frame ATG codons. In contrast, no influence on translation was found when additional sequences at the 3' end were present or when the stop codon was missing. Capping of transcripts was essential for translation in wheat germ lysates, whereas protein synthesis in reticulocytes was only reduced in the absence of a cap. The influence of polyadenylation on translation was studied using transcripts with engineered poly(A) tracts of different size. Increasing poly(A) chain length abolished translation in vitro in both translation systems. Inhibition was poly(A)-specific and is discussed as interference of the poly(A) sequences with a crucial component(s) of the protein synthesis machinery.

Bacteriophages↗
PubMed1980

Isolation and characterization of ovine prolactin and growth-hormone messenger RNAs.

Methods are described in this paper for obtaining and characterizing highly enriched preparations of ovine prolactin (PRL) and growth-hormone (GH) messenger RNAs. Purification steps include phenol extraction, oligo-(dT)-cellulose chromatography, sucrose-gradient ultracentrifugation, and polyacrylamide-gel electrophoresis. This sequence of procedures results in messenger preparations that are about 92% pure for prolactin mRNA and 78% pure for the growth-hormone mRNA species. Thus, these two closely related mRNAs can be isolated from the same tissue source at a purity adequate for cloning and nucleic acid hybridization experiments. Translation experiments with the cap analogue 7-methylguanosine, and end-labeling of the nucleic acid before and after beta-oxidation indicate that both messages possess blocked 5'-termini, and that these are part of previously described cap structures. Polyadenosine tracts of 30-160 residues were found at the 3'-ends of both purified species. Finally, sizing experiments suggest both mRNAs contain approx. 30% more bases than accounted for by the coding regions and the poly(A)-tracts. Their physical characteristics thus agree with those of most eucaryotic messages to date.

Animals↗
PubMed1984

Uteroglobin mRNA from the lung of the hare (Lepus capensis): cell-free translation and properties.

Poly(A)-containing RNA was obtained from the lung of hares (Lepus capensis) and uteroglobin mRNA was characterized by cell-free translation and molecular hybridization to a rabbit uteroglobin cDNA probe. In the cell-free system, hare uteroglobin mRNA was preferentially translated as compared to the whole lung mRNA and it directed the synthesis of a precursor, preuteroglobin, containing about twenty additional amino acids. Hare uteroglobin mRNA was about 40 nucleotides larger than the homologous rabbit one, as analyzed by electrophoresis on agarose gel. Thermal stability of the hybrids formed between rabbit or hare uteroglobin mRNAs and the rabbit cDNA probe indicated differences in the nucleotide sequence of both mRNAs. The levels of uteroglobin mRNA and uteroglobin synthesis in lung are about two-fold higher in hare than in rabbit lung.

Animals↗
PubMed2005

mRNA transfection of dendritic cells: synergistic effect of ARCA mRNA capping with Poly(A) chains in cis and in trans for a high protein expression level.

The occurrence of translation mechanism in the cytosol offers advantages to mRNA transfer over DNA-based transfection in non-dividing cells. Here, we sought to optimize mRNA constructs allowing a high level of protein upon lipofection. We found that luciferase into mouse dendritic cells (JAWSII cells) was approximately 20-fold higher when the luciferase mRNA was capped with 3'-O-methyl-m7(5')Gppp5'G (anti-reverse cap analogue; ARCA) than with m7(5')Gppp5'G (CAP). Adding a Poly(A) tail of 100 instead of 64 adenosines in cis increased by approximately 35-fold more the protein level. Finally, ARCA-Luc-mRNA-A100 construct was 700-fold better efficient than the CAP-Luc-mRNA-A64 one. Moreover, co-transfection with free Poly(A) chains in trans enhanced by 100% the luciferase level. The efficiency of ARCA-mRNA-A100 construct was validated in immature and mature human CD34-derived dendritic cells. Such mRNA construct was also successful to obtain high level of MART-1 tumor antigen.

Animals↗
PubMed2006

Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies.

The eukaryotic "scavenger" type decapping enzyme, an m(7)GpppX pyrophosphatase, is active in cellular mRNA metabolism and thereby influences posttranscriptional gene expression. The yeast version of this enzyme, Dcs1, catalyses cleavage of 5'end m(7)G-oligoribonucleotide fragments generated by 3'-->5' exonucleolytic decay, and cleavage of m(7)GDP generated by Dcp1/Dcp2-mediated decapping in the 5'-->3' decay pathway. We show that Dcs1 is active as a homodimer with low KM values for cleavage of m(7)GpppG (0.14 microM) and m(7)GDP (0.26 microM). Previous work showed that the paralogous DCS2 gene is transcriptionally induced via the amp-PKA pathway as yeast enters diauxie. The resulting Dcs2 protein forms a heterodimer together with Dcs1, both modulating Dcs1 substrate specificity and suppressing its k(cat). Since Dcs2 is recruited into cytoplasmic P bodies, its inhibitory function may be focused in these centres of mRNA storage/turnover. Dcs2 is therefore a novel type of stress-induced regulatory protein that modulates m(7)GpppX pyrophosphatase activity. Moreover, inhibition of Dcs1 activity by Dcs2, like depletion of Dcs1, reduces chronological life span, possibly by modulating m(7)G misincorporation into nucleic acids. This could potentially link control of mRNA metabolism with senescence.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Cocrystal structure of the messenger RNA 5' cap-binding protein (eIF4E) bound to 7-methyl-GDP.

The X-ray structure of the eukaryotic translation initiation factor 4E (eIF4E), bound to 7-methyl-GDP, has been determined at 2.2 A resolution. eIF4E recognizes 5' 7-methyl-G(5')ppp(5')N mRNA caps during the rate-limiting initiation step of translation. The protein resembles a cupped hand and consists of a curved, 8-stranded antiparallel beta sheet, backed by three long alpha helices. 7-methyl-GDP binds in a narrow cap-binding slot on the molecule's concave surface, where 7-methyl-guanine recognition is mediated by base sandwiching between two conserved tryptophans, plus formation of three hydrogen bonds and a van der Waals contact between its N7-methyl group and a third conserved tryptophan. The convex dorsal surface of the molecule displays a phylogenetically conserved hydrophobic/acidic portion, which may interact with other translation initiation factors and regulatory proteins.

Binding Sites↗
PubMed2002

Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action.

mTOR controls cell growth, in part by regulating p70 S6 kinase alpha (p70alpha) and eukaryotic initiation factor 4E binding protein 1 (4EBP1). Raptor is a 150 kDa mTOR binding protein that also binds 4EBP1 and p70alpha. The binding of raptor to mTOR is necessary for the mTOR-catalyzed phosphorylation of 4EBP1 in vitro, and it strongly enhances the mTOR kinase activity toward p70alpha. Rapamycin or amino acid withdrawal increases, whereas insulin strongly inhibits, the recovery of 4EBP1 and raptor on 7-methyl-GTP Sepharose. Partial inhibition of raptor expression by RNA interference (RNAi) reduces mTOR-catalyzed 4EBP1 phosphorylation in vitro. RNAi of C. elegans raptor yields an array of phenotypes that closely resemble those produced by inactivation of Ce-TOR. Thus, raptor is an essential scaffold for the mTOR-catalyzed phosphorylation of 4EBP1 and mediates TOR action in vivo.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Fluorescence and NMR studies of intramolecular stacking of mRNA cap-analogues.

Intramolecular stacking of a series of new synthesized dinucleotide mRNA cap analogues has been investigated in aqueous buffers by means of fluorescence and 1H-NMR at various pH and temperatures, and compared with that for 7-methylguanosine(5')ppp(5')guanosine (m7GpppG), as well as its hypermethylated derivative m(3)2,2,7GpppG. Thermodynamic parameters for intramolecular self-association stabilized by stacking were established by temperature-dependent fluorescence quenching, taking into account collisional deactivation of the excited states. Relative orientations of the stacked bases in the cap analogues were determined with the aid of a program GEOSHIFT (Stolarski et al., Biochim. Biophys. Acta (1996) 1293, 97), based on ring-current anisotropy. 1D-soft-TOCSY experiments were applied to extract the exact values of vicinal coupling constants, and hence to resolve solution conformation of the cap molecules. Stacking interaction has been discussed in detail in terms of the cap structural features, e.g., types of bases and length of the 5',5'-phosphate bridges, and regarding the interactions stabilizing intramolecular stacking.

Hydrogen-Ion Concentration↗
PubMed1991

Interaction of wheat germ protein synthesis initiation factors eIF-3, eIF-(iso)4F, and eIF-4F with mRNA analogues.

The interaction of wheat germ eIF-3 with the wheat germ cap-binding proteins eIF-(iso)4F and eIF-4F as a function of pH and ionic strength is described. Direct fluorescence titration experiments are used to measure the equilibrium association constants (Keq) for the binary protein/protein complexes as well as for the interaction of eIF-3 with methylated cap analogues and rabbit alpha-globin mRNA oligonucleotide analogues. The Keq values for ternary eIF-3/eIF-(iso)4F/analogue and eIF-3/eIF-4F/analogue interactions were also measured. The equilibrium binding constants were used to calculate coupling free energies, which provide an estimate of the cooperativity for the interaction of the mRNA analogues, eIF-3, and either eIF-4F or eIF-(iso)4F. These data suggest a mechanism in which the binding of eIF-(iso)4F or eIF-4F to mRNA enhances the subsequent binding of eIF-3 to the message. This may lead to favorable positioning of the complex on the ribosome and thereby enhance translation.

Animals↗
PubMed1987

Characterization of the internal initiation of translation on the vesicular stomatitis virus phosphoprotein mRNA.

Internal initiation of translation on the vesicular stomatitis virus (VSV) phosphoprotein (P) mRNA leads to the synthesis of a second protein [Herman, R. C. (1986) J. Virol. 58, 797-804]. Characterization of this phenomenon shows that initiation at the 5'-proximal and internal AUG codons has different optima for mono- and divalent cations in the reticulocyte lysate. Whereas 5' initiation is stimulated by increasing concentration of K+ over the endogenous level, internal initiation is inhibited. Internal initiation is much less sensitive to the effects of the cap analogue 7mGpppG in both the reticulocyte lysate and the wheat-germ extract under conditions that reduce 5'-proximal initiation to only about 4-5% of the control level. These results imply that 5'-proximal and internal initiations are distinct biochemical processes.

Animals↗
PubMed2004

Thermodynamics of mRNA 5' cap binding by eukaryotic translation initiation factor eIF4E.

Translation of mRNA in eukaryotes begins with specific recognition of the 5' cap structure by the highly conserved protein, eIF4E. The thermodynamics of eIF4E interaction with nine chemical cap analogues has been studied by means of emission spectroscopy. High-sensitivity measurements of intrinsic protein fluorescence quenching upon cap binding provided equilibrium association constants in the temperature range of 279 to 314 K. A van't Hoff analysis yielded the negative binding enthalpies for the entire cap analogue series, -16.6 to -81 kJ mol(-1), and the entropies covering the range of +40.3 to -136 J mol(-1) K(-1) at 293 K. The main enthalpic contributions come from interactions of the phosphate chains and positively charged amino acids and the cation-pi stacking of 7-methylguanine with tryptophans. A nontrivial, statistically important isothermal enthalpy-entropy compensation has been detected (T(c) = 399 +/- 24 K), which points to significant fluctuations of apo-eIF4E and indicates that the cap-binding microstate lies 9.66 +/- 1.7 kJ mol(-1) below the mean energy of all available conformational states. For five cap analogues, large and positive heat capacity changes have been found. The values of DeltaC(p) degrees correlate with the free energies of eIF4E binding due to stiffening of the protein upon interaction with cap analogues. At biological temperatures, binding of the natural caps has both favorable enthalpy and favorable entropy. Thermodynamic coupling of cap-eIF4E association to intramolecular self-stacking of dinucleotide cap analogues strongly influences the enthalpies and entropies of the binding, but has a negligible effect on the resultant DeltaG degrees and DeltaC(p) degrees values.

Animals↗
PubMed1999

Quantitative assessment of mRNA cap analogues as inhibitors of in vitro translation.

Fifty-eight analogues of the 5'-terminal 7-methylguanosine-containing cap of eukaryotic messenger RNA were synthesized and tested for their ability to inhibit in vitro protein synthesis. A new algorithm was developed for extracting KI, the dissociation constant for the cap analogue.eIF4E complex, from protein synthesis data. The results indicated that addition of a methyl group to the N2 of guanine produced more inhibitory compounds, but addition of a second methyl group to N2 decreased the level of inhibition dramatically. Aryl substitution at N7 improved the efficacy of guanine nucleoside monophosphate analogues. Substitution of the aromatic ring at the para position with methyl or NO2 groups abolished this effect, but substitution with Cl or F enhanced it. By contrast, aryl substitution at N7 in nucleoside di- or triphosphate analogues produced only minor effects, both positive and negative. By far the strongest determinants of inhibitory activity for cap analogues were phosphate residues. The beneficial effect of more phosphate residues was related more to anionic charge than to the number of phosphate groups per se. The second nucleotide residue in analogues of the form m7GpppN affected inhibitory activity in the order G > C > U > A, but there was no effect of 2'-O-modification. Opening the first ribose ring of m7GpppG analogues dramatically decreased activity, but alterations at the 2'-position of this ribose had no effect. Non-nucleotide-based cap analogues containing benzimidazole derivatives were inhibitory, though less so than those containing 7-methylguanine.

Animals↗
PubMed2006

A general RNA-capping ribozyme retains stereochemistry during cap exchange.

Numerous natural and artificial ribozymes have been shown to facilitate reactions that invert stereochemistry. Here, we demonstrate that an RNA-capping ribozyme retains stereochemistry at a phosphorus reaction center. The ribozyme synthesizes a broad range of 5'-5' RNA caps by exchanging phosphate groups around the alpha-phosphate found at the 5' terminus of the ribozyme. A ribozyme prepared with an Rp adenosine(5')alpha-thiotetraphosphate cap was found to exchange this cap for an Rp 4-thiouridine(5')alpha-thiotetraphosphate cap when incubated with 4-thiouridine triphosphate. The same Rp capped construct, when incubated with [gamma-(32)P]-ATP, exchanged the unlabeled ATP for a radiolabeled one while maintaining the same stereoconfiguration. In contrast, ribozymes prepared with an Sp cap failed to react even in the presence of thiophilic metal ions such as manganese. The kinetics of capping was also unusual as compared to inverting ribozymes. When the ribozyme was prepared with a triphosphate, capping was found to follow Michaelis-Menten-type kinetics even though the rate of pyrophosphate release was completely independent of nucleotide substrate concentration. Interestingly, the rate of capping and hydrolysis, when summed, was found to be indistinguishable from the rate of pyrophosphate release, indicating that an early rate-limiting step precedes both capping and hydrolysis. Together the retention of stereochemistry and kinetics imply that capping utilizes two inverting chemical steps that are separated by the transient formation of a rate-limiting covalent intermediate. As all protein enzymes that mediate similar capping reactions utilize a covalent intermediate, chemical necessity may have strongly guided the evolution of both protein and RNA-capping catalysts.

Adenosine Triphosphate↗