Antibiotics and compounds affecting translation by eukaryotic ribosomes. Specific enhancement of aminoacyl-tRNA binding by methylxanthines

Summary The mode and site of action of inhibitors of translation (initiation, elongation and termination of protein synthesis) in eukaryotic systems is reviewed. The isolation and characterization of a factor is described that binds Ac-Phe-tRNA to form a complex made up of binding factor, Ac-Phe-tRNA, and ribosome. The binding of Ac-Phe-tRNA probably occurs at the ribosomal site involved in the binding of the initiator substrate Met-tRNA_F. The effect of inhibitors of the initiation phase of protein synthesis on the nonenzymic Ac-Phe-tRNA binding to ribosomes is investigated. The two sites translocation model for translation in eukaryotic cells is presented and the effects of inhibitors on the various steps of protein synthesis are determined empirically. The site of action of inhibitors of peptide bond formation at the ribosomal peptidyl transferase center is elucidated. The action of inhibitors of translocation is studied in model cell-free systems from human cells. In addition, a number of methylxanthines are shown to enhance the elongation phase in polypeptide synthesis by stimulating the enzymic binding of aminoacyl-tRNA. The effect of caffeine, theophylline and its derivatives are shown to be fairly specific and dependent on the ribosome concentration. Aminophylline is shown to have a similar effect but also enhances aminoacyl-tRNA synthetase activity at low Mg^{+ +} concentrations, probably by displacing the optimal concentration of Mg^{+ +} in the reaction. This second effect of aminophylline appears to be due to the ethylenediamine moiety of aminophylline since it is also observed in the presence of different polyamines but not in the presence of caffeine or theophylline.An invited article.     

Effect of polyamines on synthesis and degradation of guanosine 5′-diphosphate 3′-diphosphate

The effect of polyamines on the in vitro and in vivo synthesis and degradation on guanosine 5′-diphosphate 3′-diphosphate (ppGpp) has been studied in Escherichia coli. The presence of 2 mM spermidine lowered the optimal Mg²⁺ concentration for ppGpp formation from 17 mM to 11 mM. The formation of ppGpp in the presence of 2 mM spermidine and 11 mM Mg²⁺ was about 15% greater than that in the presence of 17 mM Mg²⁺. At a concentration of less than 11 mM Mg²⁺, spermidine was found to stimulate ppGpp formation greatly. Putrescine did not cause any effect. When a polyamine-requiring mutant of E. coli (EWH319) was starved for an amino acid by the addition of valine, spermidine stimulated ppGpp formation. the degradation of ppGpp was not influenced significantly by polyamines.     

Tuber formation and development of <Emphasis Type="Italic">Dioscorea cayenensis–Dioscorea rotundata</Emphasis> complex <Emphasis Type="Italic">in vitro</Emphasis> effect of polyamines

Tuberisation was obtained in vitro on yam (Dioscorea cayenensis–Dioscorea rotundata complex). The effect of exogenous polyamines on tuber formation and development (length and weight of microtubers) was investigated and discussed in relation with changes in endogenous polyamines. Application of exogenous polyamines, inhibitors of their metabolism, and polyamines precursors in various concentrations positively affected microtuber formation by yam nodal cuttings and their further development. In control conditions, 3 wk are needed to obtain 100% of tuberisation. With low concentrations of putrescine (10⁻⁵ or 10⁻⁶ M), tuber formation occurred earlier. Polyamine endogenous level and metabolism can be significantly affected by exogenous polyamines, but modifications of endogenous free polyamines could not be directly correlated to the tuber formation process. Increases in endogenous putrescine and auxins were observed in tubers showing a better development in the presence of putrescine. These results can be used for optimising in vitro conditions for mass production of larger microtubers of the D. cayenensis–D. rotundata complex.     

Coordination of Mn++ ions at contact sites between tRNA and aminoacyl-tRNA synthetase.

By means of PMR and ESR study the shielding of Mn⁺⁺ ions by aminoacyl-tRNA synthetase has been detected in the aminoacyl-tRNA synthetase - tRNA complex at pH 7.5. At pH 6 this effect was not observed. We propose that ions interact with certain aminoacyl-tRNA synthetase groups protonated when passing to slightly acid pH. The role of Mn⁺⁺ and Mg⁺⁺ ions in the formation of a functionally active complex tRNA-aminoacyl-tRNA synthetase is discussed.     

Stimulation of valyl- and isoleucyl-tRNA synthetase reactions by polyamines

The aminoacylation of tRNA catalysed by valyl-tRNA synthetase (EC 6.1.1.9) and isoleucyl-tRNA synthetase (EC 6.1.1.5) fromMycobacterium smegmatis is dependent on the presence of divalent metal ions. Polyamines alone, in the absence of metal ions, do not bring about aminoacylation. In the presence of suboptimal concentrations of Mg²⁺, polyamines significantly stimulate the reaction. Of the cations tested, only Mn²⁺, Co²⁺ and Ca²⁺ can partially substitute for Mg²⁺ in aminoacylation, and spermine stimulates aminoacylation in the presence of these cations also. At neutral pH, spermine deacylates nonenzymatically aminoacyl tRNA. AMP and pyrophosphate-dependent enzymatic deacylation of aminoacyl-tRNA (reverse reaction) is also stimulated by spermine. The inhibitory effect of high concentration of KC1 on aminoacylation is counteracted, by spermine. The low level of activity between pH 8.5–9.0 at 1.2 mM Mg²⁺ is restored to normal level on the addition of spermine. The inhibitory effect of high pH on aminoacylation in the presence of low concentration of Mg²⁺ is also prevntedvby spemine.     

Polyamine prevention of inhibition of rat liver isoleucyl-tRNA formation by poly(G), poly(I) or ribosomes.

It is shown that rat liver isoleucyl-tRNA formation in the presence of Mg²⁺ is inhibited by poly(G), poly(I) or ribosomes and that this inhibition is prevented by polyamines. The inhibition is found to be noncompetitive with respect to tRNA.     

The role of polyamines, Na(+) and K(+) in the formation of triple helices between purine oligonucleotides and the promoter region of the human c-src proto-oncogene

Binding constants for triplex formation between purine-rich oligonucleotides and a pyrimidine·purine tract of the human c-src proto-oncogene were measured by fluorescence polarization in the presence of polyamines, Na⁺ and K⁺. In both the hexamine and tetramine series, the longer polyamines had the larger binding constants for triplex formation at low concentrations of polyamine. At higher concentrations all values tended to plateau in the 10⁹/M range. In contrast to previous reports, K⁺ did not inhibit triplex formation and at 150 mM the binding constants were again in the 10⁹/M range for both an 11mer and 22mer oligonucleotide. At 150 mM K⁺ the addition of polyamines did not lead to any significant increase in the binding constants. It was determined that the lack of inhibition by K⁺ was due to the low concentration (1 nM) of purine oligonucleotide required for the fluorescence polarization technique. At higher concentrations (1 µM) self-association of the oligonucleotide was observed. These results suggest that in vivo, at least for the c-src promoter, the inhibition of triplex formation by K⁺ may not be detrimental. However, it may be difficult to achieve binding constants above ~10⁹/M even in the presence of polycations.     

Polyamines and amino acid incorporation in vitro into microsomes of rat cerebral cortex

1. Polyamines were found to be associated with microsomes of rat cerebral cortex, the amount of spermine being about four times that of spermidine. Cell sap contained more spermidine than spermine. 2. Both polyamines were able to stimulate the incorporation of [(14)C]valine into microsomes in vitro with a maximum rate equal to 250% of the control. Polyamines stimulated at concentrations close to the amount of spermine and spermidine naturally present in the system. 3. Spermine (0.05mm) was used to study the mechanism of action of polyamines. The increasing of microsome and cell-sap concentration facilitated the action of spermine, but the same process was inhibited by increasing pH5-enzyme concentration. 4. Spermine did not affect the association of [(14)C]valine with tRNA in cell sap, but increased the rate of aminoacyl-tRNA formation in pH5 enzyme preparations. However, this process was not affected in any case when incorporating microsomes were present. 5. It is suggested that microsomes are the main site of action of polyamines.     

Unique polyamines produced by an extreme thermophile, <Emphasis Type="Italic">Thermus thermophilus</Emphasis>

Summary. Recent research progress on polyamines in extreme thermophiles is reviewed. Extreme thermophiles produce two types of unique polyamines; one is longer polyamines such as caldopentamine and caldohexamine, and the other is branched polyamines such as tetrakis(3-aminopropyl)ammonium. The protein synthesis catalyzed by a cell-free extract of Thermus thermophilus, an extreme thermophile, required the presence of a polyamine and the highest activity was found in the presence of tetrakis(3-aminopropyl)ammonium. In vitro experiments, longer polyamines efficiently stabilized double stranded nucleic acids and a branched polyamine, tetrakis(3-aminropyl)ammonium, stabilized stem-and-loop structures. In T. thermophilus, polyamines are synthesized from arginine by a new metabolic pathway; arginine is converted to agmatine and then agmatine is aminopropylated to N¹-aminopropylagmatine which is converted to spermidine by an enzyme coded by a gene homologous to speB (a gene for agmatinase). In this new pathway spermidine is not synthesized from putrescine. Reverse genetic studies indicated that the unique polyamines are synthesized from spermidine.     

Oligogalacturonides enhance cytokinin-induced vegetative shoot formation in tobacco explants, inhibit polyamine biosynthetic gene expression, and promote long-term remobilisation of cell calcium

Long-sized oligogalacturonides (OGs) are cell wall fragments that induce defence and developmental responses. The Ca²⁺-dependent “egg-box” conformation is required for their activity, and polyamines may prevent them from adopting this conformation. Although OGs are known to inhibit auxin-induced growth processes, their effect on cytokinin-induced ones requires investigation. In the present work OGs were shown to promote cytokinin (benzyladenine, BA)-induced vegetative shoot formation from tobacco leaf explants, independent of the presence of CaCl₂ in the medium and of auxin (indoleacetic acid, IAA) supply. The effect of polyamines, putrescine (PU) and spermidine (SD) supplied with/without their biosynthetic inhibitors (DFMO, CHA) was also investigated, and showed that spermidine enhanced adventitious vegetative shoot formation, but only on medium containing Ca²⁺ and IAA. Treatments with inhibitors blocked this promotive effect. OGs did not alter free polyamine concentrations, but caused a moderate increase of conjugated ones, and exhibited an early inhibitory effect on polyamine biosynthetic gene expression. OGs, but not SD, caused long-term changes in calcium-associated epifluorescent signals in the cell walls, and, later, inside the cells of specific tissues. Electron microscopy analysis (ESI system) demonstrated that calcium accumulated in the cell walls and vacuoles of OG-cultured explants. The relationship between OGs, cytokinin, calcium, and polyamines in adventitious vegetative shoot formation is discussed.     

Conjugation with polyamines enhances the antibacterial and anticancer activity of chloramphenicol

Chloramphenicol (CAM) is a broad-spectrum antibiotic, limited to occasional only use in developed countries because of its potential toxicity. To explore the influence of polyamines on the uptake and activity of CAM into cells, a series of polyamine–CAM conjugates were synthesized. Both polyamine architecture and the position of CAM-scaffold substitution were crucial in augmenting the antibacterial and anticancer potency of the synthesized conjugates. Compounds 4 and 5, prepared by replacement of dichloro-acetyl group of CAM with succinic acid attached to N4 and N1 positions of N⁸,N⁸-dibenzylspermidine, respectively, exhibited higher activity than CAM in inhibiting the puromycin reaction in a bacterial cell-free system. Kinetic and footprinting analysis revealed that whereas the CAM-scaffold preserved its role in competing with the binding of aminoacyl-tRNA 3′-terminus to ribosomal A-site, the polyamine-tail could interfere with the rotatory motion of aminoacyl-tRNA 3′-terminus toward the P-site. Compared to CAM, compounds 4 and 5 exhibited comparable or improved antibacterial activity, particularly against CAM-resistant strains. Compound 4 also possessed enhanced toxicity against human cancer cells, and lower toxicity against healthy human cells. Thus, the designed conjugates proved to be suitable tools in investigating the ribosomal catalytic center plasticity and some of them exhibited greater efficacy than CAM itself.     

Intermediate reactions in the binding of aminoacyl-transfer ribonucleic acid to rat liver ribosomes. The role of guanosine triphosphate

1. Transferase I from rat liver binds relatively low quantities of GTP when incubated with this nucleotide in the absence of aminoacyl-tRNA. 2. Transferase I reacts with both aminoacyl-tRNA and GTP to form a relatively stable complex that is retained on cellulose nitrate filters. The ternary complex transferase I-aminoacyl-tRNA-GTP is also formed when the transferase I-aminoacyl-tRNA complex is incubated with GTP or during the incubation of the transferase I-GTP complex with aminoacyl-tRNA. Synthesis of this complex does not require the presence of Mg(2+). 3. In the presence of Mg(2+) the ternary complex becomes readily bound to ribosomes without requirements for any other cofactors. 4. An extensive cleavage of GTP takes place when aminoacyl-tRNA becomes bound to ribosomes. 5. The low interdependence of reactions leading to the formation of transferase I complexes with aminoacyl-tRNA and GTP indicates that the mechanisms of the binding reaction in mammalian systems may be different from those in bacterial cells.     

Myocardial aminoacyl-transfer-ribonucleic acid synthetase and aminoacyl-transferring enzyme activity

The properties of cytoplasmic aminoacyl-tRNA synthetase and aminoacyl-transferring enzymes in the myocardium were examined and methods for the assay of the activity of these enzyme systems were developed. Aminoacyl-tRNA synthetase activity was measured from the rate of incorporation of ¹⁴C-labelled amino acid into aminoacyl-tRNA. Transferase activity was measured from the rate of incorporation of amino[¹⁴C]acyl-tRNA into protein in the presence of a standard preparation of hepatic ribosomes. Aminoacyl-tRNA synthetase activity is labile once the heart has been homogenized, whereas transferase activity is stable. The source of energy for synthetase activity is ATP; that for transferase is GTP. Transferase activity was inhibited by puromycin and stimulated by dithiothreitol, whereas synthetase activity was unaffected.     

Two-step aminoacylation of tRNA without channeling in Archaea

Catalysis of sequential reactions is often envisaged to occur by channeling of substrate between enzyme active sites without release into bulk solvent. However, while there are compelling physiological rationales for direct substrate transfer, proper experimental support for the hypothesis is often lacking, particularly for metabolic pathways involving RNA. Here, we apply transient kinetics approaches developed to study channeling in bienzyme complexes to an archaeal protein synthesis pathway featuring the misaminoacylated tRNA intermediate Glu-tRNA^Gln. Experimental and computational elucidation of a kinetic and thermodynamic framework for two-step cognate Gln-tRNA^Gln synthesis demonstrates that the misacylating aminoacyl-tRNA synthetase (GluRS^ND) and the tRNA-dependent amidotransferase (GatDE) function sequentially without channeling. Instead, rapid processing of the misacylated tRNA intermediate by GatDE and preferential elongation factor binding to the cognate Gln-tRNA^Gln together permit accurate protein synthesis without formation of a binary protein-protein complex between GluRS^ND and GatDE. These findings establish an alternate paradigm for protein quality control via two-step pathways for cognate aminoacyl-tRNA formation.     

Evidence of different G-quadruplex DNA binding with biogenic polyamines probed by electrospray ionization-quadrupole time of flight mass spectrometry,circular dichroism and atomic force microscopy

The binding properties of five G-quadruplex oligonucleotides (humtel24, k-ras32, c-myc22, c-kit1 and c-kit2) with polyamines have been investigated by electrospray ionization-quadrupole time of flight mass spectrometry, circular dichroism, melting temperature, atomic force microscopy (AFM) and molecular simulation. The MS results demonstrated that the polyamines and G-quadruplex DNA can form complexes with high affinity, and one molecule of G-quadruplex DNA can combine several molecules (1–5) of polyamines. The binding affinities of the polyamines to DNA were in the order of spermine > spermidine > putrescine. After binding with polyamines, the conformations of the G-quadruplex DNA were significantly changed, and spermine can induce the configurations of k-ras32 and c-kit1 to deviate from their G-quadruplex structures at high concentrations. In the presence of K⁺, the conformations of G-quadruplex DNA were stabilized, while polyamines can also induced alterations of their configurations. Melting temperature experiments suggested that the T_m of the DNA–polyamine complexes obviously increased both in the absence and presence of K⁺. The AFM results indicated that polyamines can induce aggregation of G-quadruplex DNA. Above results illustrated that the polyamines bound with the phosphate backbone and the base-pairs of G-quadruplex structures. Combining with the molecular simulation, the binding mode of the G-quadruplex DNA and polyamines were discussed. The results obtained would be beneficial for understanding the biological and physiological functions of polyamines and provide useful information for development of antitumor drugs.     

Regulation by the exogenous polyamine spermidine of Na,K-ATPase activity from the gills of the euryhaline swimming crab Callinectes danae (Brachyura, Portunidae)

Euryhaline crustaceans rarely hyporegulates and employ the driving force of the Na,K-ATPase, located at the basal surface of the gill epithelium, to maintain their hemolymph osmolality within a range compatible with cell function during hyper-regulation. Since polyamine levels increase during the adaptation of crustaceans to hyperosmotic media, we investigate the effect of exogenous polyamines on Na,K-ATPase activity in the posterior gills of Callinectes danae, a euryhaline swimming crab. Polyamine inhibition was dependent on cation concentration, charge and size in the following order: spermine > spermidine > putrescine. Spermidine affected K_0.5 values for Na⁺ with minor alterations in K_0.5 values for K⁺ and NH₄⁺, causing a decrease in maximal velocities under saturating Na⁺, K⁺ and NH₄⁺ concentrations. Phosphorylation measurements in the presence of 20 µM ATP revealed that the Na,K-ATPase possesses a high affinity site for this substrate. In the presence of 10 mM Na⁺, both spermidine and spermine inhibited formation of the phosphoenzyme; however, in the presence of 100 mM Na⁺, the addition of these polyamines allowed accumulation of the phosphoenzyme. The polyamines inhibited pumping activity, both by competing with Na⁺ at the Na⁺-binding site, and by inhibiting enzyme dephosphorylation. These findings suggest that polyamine-induced inhibition of Na,K-ATPase activity may be physiologically relevant during migration to fully marine environments.     

Interaction of polyamines with fragments and whole molecules of yeast phenylalanine-specific transfer RNA

Binding of the polyamines spermidine (∼-+3) and spermine (∼-+4) to yeast tRNA^phe has been investigated by equilibrium dialysis under the same conditions used to study Mn²⁺-tRNA^phe interactions (Schreier & Schimmel, 1974). The polyamines bind to tRNA^phe in a co-operative and a non-co-operative phase, which is analogous to the behavior found with Mn²⁺. In the co-operative phase, the empirical index of co-operativity is somewhat greater for the polyamines, however. Binding constants for both the co-operative and non-co-operative phases are similar for Mn²⁺ and spermidine, and are strongest for spermine. Estimates of the total number of ligand binding sites indicate that these numbers are inversely proportional to the charge on the ligand for all three ligands. The interaction of polyamines with four large fragments of tRNA^phe shows no evidence for co-operativity. These results, together with recent kinetic studies, collectively suggest that polyamine binding to the co-operative sites is associated with tertiary structure formation and that polyamine and divalent metal ion interactions with tRNA occur by phenomenologically similar mechanisms, in spite of their structural diversity.     

Polyamines stimulate the formation of mutagenic 1,N2-propanodeoxyguanosine adducts from acetaldehyde

Alcoholic beverage consumption is associated with an increased risk of upper gastrointestinal cancer. Acetaldehyde (AA), the first metabolite of ethanol, is a suspected human carcinogen, but the molecular mechanisms underlying AA carcinogenicity are unclear. In this work, we tested the hypothesis that polyamines could facilitate the formation of mutagenic α-methyl-γ-hydroxy-1,N²-propano-2′-deoxyguanosine (Cr-PdG) adducts from biologically relevant AA concentrations. We found that Cr-PdG adducts could be formed by reacting deoxyguanosine with μM concentrations of AA in the presence of spermidine, but not with either AA or spermidine alone. The identities of the Cr-PdG adducts were confirmed by both liquid and gas chromatography-mass spectrometry. Using a novel isotope-dilution liquid chromatography-mass spectrometry assay, we found that in the presence of 5 mM spermidine, AA concentrations of 100 μM and above resulted in the formation of Cr-PdG in genomic DNA. These AA levels are within the range that occurs in human saliva after alcoholic beverage consumption. We also showed that spermidine directly reacts with AA to generate crotonaldehyde (CrA), most likely via an enamine aldol condensation mechanism. We propose that AA derived from ethanol metabolism is converted to CrA by polyamines in dividing cells, forming Cr-PdG adducts, which may be responsible for the carcinogenicity of alcoholic beverage consumption.     

Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure

The effects of ions (i.e. Na⁺, Mg²⁺ and polyamines including spermidine and spermine) on the stability of various DNA oligonucleotides in solution were studied. These synthetic DNA molecules contained sequences that mimic various cellular DNA structures, such as duplexes, bulged loops, hairpins and/or mismatched base pairs. Melting temperature curves obtained from the ultraviolet spectroscopic experiments indicated that the effectiveness of the stabilization of cations on the duplex formation follows the order of spermine > spermidine > Mg²⁺ > Na⁺ > Tris–HCl buffer alone at pH 7.3. Circular dichroism spectra showed that salts and polyamines did not change the secondary structures of those DNA molecules under study. Surface plasmon resonance (SPR) observations suggested that the rates of duplex formation are independent of the kind of cations used or the structure of the duplexes. However, the rate constants of DNA duplex dissociation decrease in the same order when those cations are involved. The enhancement of the duplex stability by polyamines, especially spermine, can compensate for the instability caused by abnormal structures (e.g. bulged loops, hairpins or mismatches). The effects can be so great as to make the abnormal DNAs as stable as the perfect duplex, both kinetically and thermodynamically. Our results may suggest that the interconversion of various DNA structures can be accomplished readily in the presence of polyamine. This may be relevant in understanding the role of DNA polymorphism in cells.