The activation of amino acid analogues by phenylalanyl- and tyrosyl-tRNA synthetases from plants

Partially purified preparations of Phe- and Tyr-tRNA synthetases were obtained from seed or seedlings of Phaseolus aureus, Delonix regia and Caesalpinia tinctoria, and the ability of a variety of structural analogues of Phe or Tyr to act as alternative substrates or inhibitors was tested. 3-Hydroxymethylphenylalanine, a natural product of C. tinctoria, formed a particularly effective substrate for the Tyr-tRNA synthetase from P. aureus. The structural features commensurate with substrate activity in an analogue molecule are discussed.     

A comparison of the thermal stability and substrate binding constants of prolyl-tRNA synthetase from Phaseolus aureus and Delonix regia

Pro-tRNA synthetase from P. aureus and D. regia was protected against thermal denaturation by various substrates; the kinetics of this protection was investigated. The affinity of substrates for each synthetase was studied by a thermal inactivation technique. In the presence of ATP, Pro and several Pro-analogues were bound to each enzyme more efficiently than when ATP was absent. The efficiency of imino acid analogue binding, relative to that of Pro, was greater when ATP was absent. Pyrrolidine and 3-pyrroline were able to bind to the enzyme only in the presence of ATP. The ratio of the ATP/Pro binding constants for the Delonix enzyme was greater than that for the Phaseolus enzyme. Values for several thermodynamic parameters involved in substrate binding were determined for each synthetase. The results are discussed in relation to the order of substrate binding and the known differences in substrate specificity between the enzymes from P. aureus and D. regia.     

Cold-lability of prolyl-tRNA synthetase from higher plants

Pro-tRNA synthetase from D. regia and P. aureus lost enzymic activity more rapidly at 0° than at room temperature. The enzyme from a number of higher plants that produce azetidine-2-carboxylic acid (A2C) was more rapidly inactivated in the cold than the enzyme from plants which do not contain A2C. The rate of cold inactivation was dependent on temperature and on the concentration of glycerol, protein and sulphydryl-reducing reagents. Substrates of Pro-tRNA synthetase also stabilized the enzyme against cold inactivation. Enzyme which had been completely inactivated by storage in the cold, could be reactivated by warming in the presence of a sulphydryl-reducing reagent. The rate of reactivation was dependent on temperature, pH and the concentration of sulphydryl-reducing reagent. Kinetic analysis indicated the existence of more than one molecular form of the enzyme. It is suggested that the cold-lability of Pro-tRNA synthetase may be due to dissociation of the active enzyme molecule into inactive subunits.     

Purification and characterization of two tyrosyl-tRNA synthetase activities from soybean cotyledons

The tyrosyl-tRNA synthetases located in cytoplasm and chloroplasts of soybean cotyledons were purified to near homogeneity by ammonium sulfate precipitation, DEAE-cellulose chromatography, hydroxylapatite chromatography, and DEAE-Sephadex A-25 chromatography. Purified cytoplasmic tyrosyl-tRNA synthetase shows only a single band in acrylamide gel electrophoresis which corresponds to a MW of 126000. In SDS-acrylamide gel electrophoresis the enzyme again shows only a single band which corresponds to a MW of 61 000. Chloroplast tyrosyl-tRNA synthetase shows only one band in both acrylamide and SDS-acrylamide gel electrophoresis with MWs being 98 000 and 43 000, respectively. For cytoplasmic tyrosyl-tRNA synthetase the apparent K_ms determined are 6.8 μM L-tyrosine, 49 μM ATP, and 8.9 × 10^?8 M tRNA (as total tRNA). Apparent K_ms for chloroplast tyrosyl-tRNA synthetase are 4.9 μM L-tyrosine, 214 μM ATP and 2.2 × 10^?8 M tRNA (as BDC-ethanol fraction tRNA). Fractionation of soybean cotyledon-tRNA on RPC-5 columns gives 4 tyrosyl-tRNA species, the first two species (tRNA_{1 and 2}^Tyr) are acylated only by cytoplasmic tyrosyl-tRNA synthetase while the last two species (tRNA_{3 and 4}^Tyr) are acylated only by chloroplast tyrosyl-tRNA synthetase.     

Substrate discrimination by prolyl-tRNA synthetase from various higher plants

Prolyl-tRNA synthetase from plants (e.g. Delonix regia) containing azetidine-2-carboxylic acid (A2C), activated imino acid analogues larger than proline (Pro) more efficiently than did the enzyme from plants lacking A2C. The reverse situation was observed for analogues, including A2C itself, that are smaller than Pro. The enzyme from A2C-producing species was quite labile and salt-sensitive, with a high pH optima for the ATP-³²PPi exchange reaction, whereas the enzyme from non-producer species was stable and insensitive to salts, with a lower pH optimum. Certain analogues of Pro, which failed to stimulate ATP-³²PPi in the presence of a particular type of Pro-tRNA synthetase, nevertheless could bind to the enzyme and inhibit the esterification of tRNA by Pro. In the absence of tRNA, no significant ATP-³²PPi exchange was catalyzed by the Delonix enzyme on addition of A2C; the addition of tRNA resulted in a low but real level of activation of the analogue relative to Pro. These findings are discussed in relation to the ability of the enzyme from A2C-producing plants to discriminate against the analogue.     

Leucine specific transfer ribonucleic acids and synthetases in the cotyledons of mature and germinating pea seeds

Changes in isoaccepting species of tRNA^Leu were determined in germinating pea seedlings and in developing pods. Leucine specific transfer ribonucleic acids of pea cotyledons can be fractionated into four isoaccepting species by reversed-phase chromatography (RPC-5) on a Plaskon column. In contrast, only two species of tRNA^Leu were observed in developing seed pods. Leucyl-tRNA synthetase purified by ammonium sulfate precipitation and DEAE cellulose column chromatography retained the full range of specificity towards all four tRNA^Leu species of pea cotyledons. This partially purified pea cotyledon enzyme could be further separated on a hydroxylapatite (HA) column into two peaks of leucyl-tRNA synthetase activity. Enzyme 1 is dominant in seed pods while 2 is predominant in cotyledons. Enzymes 1 and 2 from cotyledons were examined for the amino acid acceptor activity of twelve different amino acids. Both these fractions showed less than 3% acceptor activity for eleven other amino acids as compared to leucine-tRNA synthetase activity. Preliminary characterization of enzyme 2 from cotyledon, by isoelectric focusing and polyacrylamide gel electrophoresis indicates at least three subspecies.     

Changes in leucyl-tRNAs and aminoacyl tRNA synthetases in developing and aging soybean cotyledons

Leucine specific tRNA of soybean cotyledons was frationated into six peaks (1–6). The relative amounts of Leu-tRNA 5 and 6 are lower in developing cotyledons than in germinating cotyledons. Leu-tRNA synthetase from developing cotyledons is less active in aminoacylating Leu-tRNA 5 and 6 compared to enzyme from 5-day-old germinating cotyledons. Leu-tRNA synthetase from cotyledons of germinating seedlings and developing cotyledons can be fractionated into three peaks (1–3). Peak 1 in the developing cotyledon is about 36% less than peak 1 from 5-day-old germinating cotyledons. Peaks 2 and 3 from developing cotyledons are about 10 and 18% higher than from germinating cotyledons, respectively. Peak 1 from developing cotyledons acylates all six species of Leu-tRNA in contrast with peak 1 from germinating cotyledons, which essentially acylates only Leu-tRNA 5 and 6. The specificity of peaks 2 and 3 towards Leu-tRNA 1–4 is identical in both the organs.     

Prenyl transferases from Micrococcus luteus: Characterization of undecaprenyl pyrophosphate synthetase

Three prenyl transferases in Micrococcus luteus were recovered in the soluble fraction following cell disruption. Undecaprenyl pyrophosphate (C₅₅-PP) synthetase chromatographed on DEAE-cellulose independently from geranylgeranyl-PP and octaprenyl-PP synthetases. Further purification of C₅₅-PP synthetase resulted in an approximate 250-fold purification over the crude lysate. The molecular weight of the synthetase was estimated to be between 47,000 and 49,000 by Sephadex G-100 chromatography. The enzyme had a broad specificity toward the allylic pyrophosphate substrate. The reactivities of the allylic substrates increased with chain length, C₁₀ < C₁₅ < C₂₀, except for trans-solanesyl-PP, which was unreactive. Moreover, the enzyme was active on allylic substrates having both cis- and trans-stereochemistry. Although C₅₅-PP and C₅₀-PP were the major products, some shorter chain products were also produced, when t,t-farnesyl pyrophosphate and Δ³sopentenyl pyrophosphate (IPP) were used as substrates. The stereochemistries of the products formed with C₅₅-PP synthetase were established, using [¹⁴C]IPP and 2R-[2-³H] and 2S-[2-³H]IPP. Each new isoprene unit added had a cis-configuration. The enzyme was inactive in the absence of added effectors. It was stimulated by Triton X-100, egg lecithin, and a whole phospholipid extract from M. luteus. Cardiolipin and deoxycholate were poor activators of the enzyme. The product chain length distribution observed with the phospholipid-activated enzyme showed highly favored production of the C₅₅-PP product over the C₅₀-PP product.     

Pro-tRNA synthetase from Phaseolus aureus and Delonix regia

Pro-tRNA synthetase from Phaseolus aureus was photoinactivated in the presence of methylene blue or rose bengal. Pro and several imino acid analogues protected the enzyme against dye-mediated photoinactivation but ATP was ineffective. Together with kinetic data, this evidence suggested that a His-residue near the Pro-binding site was involved in the enzyme reaction. In the absence of methylene blue, Phaseolus enzyme was stable to light whilst that from Delonix was rapidly and reversibly photoinactivated. ATP as well as Pro, protected the Delonix enzyme against dye-independent photoinactivation. In the presence of methylene blue, the Delonix enzyme was more rapidly photoinactivated than in the absence of the dye. p-Chloromercuribenzoate (pCMB)-inhibited enzyme from both Phaseolus and Delonix was reactivated by sulphydryl reducing reagents. Reactivation of Delonix enzyme was markedly temperature-dependent whilst Phaseolus enzyme was reactivated equally efficiently at all temperatures tested. ATP, tRNA, Pro and several analogues of Pro, protected both the Phaseolus and Delonix enzymes against pCMB inhibition. The possible roles of the His-residue and SH group are discussed in relation to the known differences in substrate specificity between the Phaseolus and Delonix enzymes.     

Pyrimidine nucleotide biosynthesis in Clonorchis sinensis and Paragonimus ohirai

Kobayashi M., Yokogawa M., Mori M. and Tatibana M. 1978. Pyrimidine nucleotide biosynthesis in Clonorchis sinensis and Paragonimus ohirai. International Journal for Parasitology8: 471–477. A carbamoyl phosphate synthetase was detected in the cytosol fractions of the adult worms of Clonorchis sinensis and Paragonimus ohirai. The enzyme was partially purified and was shown to utilize both l-glutamine and ammonia and does not require $\text{N-}\text{acetyl}\text{-}\text{l}\text{-}\text{glutamate}$. The enzyme was subject to specific feedback inhibition by end products such as UDP, UTP, CDP, dUDP and dCDP and was stimulated by 5-phosphoribosyl-1-pyrophosphate. These properties of the synthetase were similar to those of carbamoyl phosphate synthetase II demonstrated in mammalian tissues Some other enzyme activities of this pathway were also detected in both species. Paragonimus ohirai actively incorporated ¹⁴CO₂ into uridine nucleotides; accumulation of intermediates of the pathway was not seen. These results indicate that the carbamoyl phosphate synthetase plays a key and regulatory step of ^{de novo} pyrimidine nucleotide biosynthesis in these worms.     

Amino acid incorporation on 80s plant ribosomes: The complete system

A cell-free system directed by poly U or turnip yellow mosaic virus (TYMV)-RNA was obtained from imbibed seeds of Phaseolus aureus; this in vitro system was dependent upon exogenous tRNA. The poly U-directed system functioned in the presence of tRNAs from P. aureus, Vicia faba and yeast, whereas TYMV-RNA was translated only in the presence of tRNAs from P. aureus or V. faba. The pH and Mg²⁺ optima for aminoacylation of tRNAs of P. aureus, V. faba and yeast by leucine and phenylalanine were related to the overall pH and ionic concentration optima for the complete system.     

The Formation of beta, 1 --> 4 Glucan from UDP-alpha-d-Glucose Catalyzed by a Phaseolus aureus Enzyme

Particulate enzyme preparations from Phaseolus aureus hypocotyls catalyze the formation of an alkali insoluble β, 1 → 4 linked [¹⁴C]-glucan using UDP-α-d [¹⁴C]-glucose as substrate. Particulate enzymes prepared from root tissue also catalyzed the production of β, 1 → 4 glucan. UDP-β-d-[¹⁴C]-glucose would not serve as a substrate for these enzymes. The presence or absence of β, 1 → 4 glucan synthetase activity was independent of tissue source, substrate concentration, or homogenization method.     

On enzymic clotting processes V: Rate equations for the case of arbitrary rate of production of the clotting species

The rate theory for enzyme-triggered coagulation reactions, such as the clotting of fibrin or casein, is extended to the case of an arbitrary rate of production of the clotting species. It is shown that the general expression for the growth of the weight-average molecular weight of the clotting product, -M_w, is given by -M_w = M₁{1 + k_s {∫₀^tP(t)² dt}/P(t)}, where M₁ is the “monomer” molecular weight, k_s the smoluchowskian flocculation rate constant and P(t) the total number of monomers produced by the enzyme in t. In the purely smoluchowskian case P(t) stands for the total number of monomers at the beginning of the clotting process. Numerical examples in which the rate of enzymic production is governed by complete Michaelis-Menten kinetics, are compared to cases in which this rate equals V_max- It is shown that after exhaustion of the substrate the system continues to coagulate in a purely smoluchowskian way. Turbidimetric experiments on the clotting of micelles of whole and κ-casein are presented which suggest inactivation of the enzyme by non-productive binding in the flocs formed.     

Characterization of Two Members among the Five ADP-Forming Acyl Coenzyme A (Acyl-CoA) Synthetases Reveals the Presence of a 2-(Imidazol-4-yl)Acetyl-CoA Synthetase in Thermococcus kodakarensis

The genome of Thermococcus kodakarensis, along with those of most Thermococcus and Pyrococcus species, harbors five paralogous genes encoding putative α subunits of nucleoside diphosphate (NDP)-forming acyl coenzyme A (acyl-CoA) synthetases. The substrate specificities of the protein products for three of these paralogs have been clarified through studies on the individual enzymes from Pyrococcus furiosus and T. kodakarensis. Here we have examined the biochemical properties of the remaining two acyl-CoA synthetase proteins from T. kodakarensis. The TK0944 and TK2127 genes encoding the two α subunits were each coexpressed with the β subunit-encoding TK0943 gene. In both cases, soluble proteins with an α₂β₂ structure were obtained and their activities toward various acids in the ADP-forming reaction were examined. The purified TK0944/TK0943 protein (ACS III_Tk) accommodated a broad range of acids that corresponded to those generated in the oxidative metabolism of Ala, Val, Leu, Ile, Met, Phe, and Cys. In contrast, the TK2127/TK0943 protein exhibited relevant levels of activity only toward 2-(imidazol-4-yl)acetate, a metabolite of His degradation, and was thus designated 2-(imidazol-4-yl)acetyl-CoA synthetase (ICS_Tk), a novel enzyme. Kinetic analyses were performed on both proteins with their respective substrates. In T. kodakarensis, we found that the addition of histidine to the medium led to increases in intracellular ADP-forming 2-(imidazol-4-yl)acetyl-CoA synthetase activity, and 2-(imidazol-4-yl)acetate was detected in the culture medium, suggesting that ICS_Tk participates in histidine catabolism. The results presented here, together with those of previous studies, have clarified the substrate specificities of all five known NDP-forming acyl-CoA synthetase proteins in the Thermococcales.     

Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme

FabH (β-ketoacyl-acyl carrier protein synthase III) is unique in that it initiates fatty acid biosynthesis, is inhibited by long-chain fatty acids providing means for feedback control of the process, and dictates the fatty acid profile of the organism by virtue of its substrate specificity. We report the crystal structures of bacterial FabH enzymes from four different pathogenic species: Enterococcus faecalis, Haemophilus influenzae, Staphylococcus aureus and Escherichia coli. Structural data on the enzyme from different species show important differences in the architecture of the substrate-binding sites that parallel the inter-species diversity in the substrate specificities of these enzymes.     

Stabilization of aminoacyl-tRNA synthetases by sephadex and polyacrylamide gels

Several aminoacyl-tRNA synthetases from the yellow lupin (Lupinus luteus) were stabilized against inactivation during storage at 0–4°, by entrapment in Sephadex or Biogel matrices and drying over P₂O₅. The degree of stabilization depended on the rate of drying of the gel and the pH of the medium and to a lesser extent on the ionic strength and protein concentration. With the exception of prolyl-tRNA synthetase, a greater stability was achieved with those enzymes which were relatively stable to thermal denaturation. Aminoacyl-tRNA synthetases for glutamic acid, glutamine, methionine and arginine, which become inactivated during purification, were considerably stabilized by this procedure.     

Effects of phospholipids on substrate specificity of β-galactosidase purified from Aspergillus oryzae

When entrapped into liposomes composed of phosphatidylcholine and other lipids, β-galactosidase (β-d-galactoside galactohydrolase, EC 3.2.1.23) purified from Aspergillus oryzae could cleave the β-galactosidic bond of the terminal galactose of galactocerebroside and GM₁-ganglioside (II³NeuAc-GgOse₄Cer, galactosyl-N-acetylgalactosaminyl-(N-acetylneuraminosyl)-galactosylglucosylceramide), while the free enzyme could not. The products of the hydrolysis of galactocerebroside were found to be β-galactose and ceramide, which was confirmed by using a fluorescent analog of galactocerebroside, 1-O-galactosyl-2-N-(1-dimethylaminonaphthalene-5-sulfonyl)-sphingosine, as substrate. The formation of GM₂-ganglioside (II³NeuAc-GgOse₃Cer, N-acetylgalactosaminyl-(N-acetylneuraminosyl)-galactosylglucosylceramide) by the hydrolysis of GM₁-ganglioside was also demonstrated. The lipid composition of the liposomes influenced the amount of the enzyme entrapped and the activity of the trapped enzyme. A large amount of the enzyme was entrapped into the liposomes composed of phosphatidylcholine-cholesterol-stearoylamine (molar ratio, 7:2:1). The enzyme trapped in the liposomes and that in those of phosphatidylcholine-cholesterol-sulfatide (molar ratio, 7:2:1) had higher activity on galactocerebroside and GM₁-ganglioside than that in other liposomes. The activity of β-galactosidase trapped in liposomes was increased in the presence of detergent, while that of the free enzyme was not changed.By a similar procedure to introduce enzymes into hydrophobic environments, enzymes other than β-galactosidase might come to possess different substrate specificities.     

The Modified β-Ketoadipate Pathway in Rhodococcus rhodochrous N75: Enzymology of 3-Methylmuconolactone Metabolism

Rhodococcus rhodochrous N75 is able to metabolize 4-methylcatechol via a modified β-ketoadipate pathway. This organism has been shown to activate 3-methylmuconolactone by the addition of coenzyme A (CoA) prior to hydrolysis of the butenolide ring. A lactone-CoA synthetase is induced by growth of R. rhodochrous N75 on p-toluate as a sole source of carbon. The enzyme has been purified 221-fold by ammonium sulfate fractionation, hydrophobic chromatography, gel filtration, and anion-exchange chromatography. The enzyme, termed 3-methylmuconolactone-CoA synthetase, has a pH optimum of 8.0, a native M_r of 128,000, and a subunit M_r of 62,000, suggesting that the enzyme is homodimeric. The enzyme is very specific for its 3-methylmuconolactone substrate and displays little or no activity with other monoene and diene lactone analogues. Equimolar amounts of these lactone analogues brought about less than 30% (most brought about less than 15%) inhibition of the CoA synthetase reaction with its natural substrate.     

Isolation and properties of naphthoate synthetase from Mycobacterium phlei

Cell-free extracts obtained by sonication of Mycobacterium phlei cells contain an important enzyme of the menaquinone (= vitamin K₂) biosynthetic pathway. This enzyme, naphthoate synthetase (1,4-dihydroxy-2-naphthoate synthetase), was partially purified by chromatography on Sepharose 6BCL. Conversion of o-succinylbenzoate to 1,4-dihydroxy-2-naphthoate was followed by a radioactivity assay using o-[2,3-¹⁴C₂]succinylbenzoate, or by a spectrophotofluorometric assay. o-[1-¹³C]Succinylbenzoate was converted intact by the extracts to dihydroxynaphthoate containing ¹³C only in the carboxyl carbon atom. For maximum activity, the enzyme requires ATP, Mg²⁺, and coenzyme A. The pH optimum is 6.9 and the molecular weight approximately 44,000. In the presence of farnesyl pyrophosphate, the extracts convert o-[2,3-¹⁴C₂]succinylbenzoate to ¹⁴C-containing menaquinone.     

Inhibition of Escherichia coli glutamine synthetase by phosphinothricin

The inhibition of Escherichia coli glutamine synthetase by phosphinothricin [2-amino-4-(methylphosphinyl)butanoic acid] has been studied. This amino acid was observed to function as an active site directed inhibitor exhibiting time-dependent inhibition of glutamine synthetase in the presence of ATP or adenylylimidodiphosphate (AMPPNP) but not adenylyl(β,γ-methylene) diphosphonate (AMPPCP). The inactivation was observed to be pseudo-first order. Phosphinothricin was also found to inhibit the enzyme reversibly under initial rate conditions and was competitive with respect to glutamate with K_1S = 18 ± 3 μm. The inactive enzyme inhibitor complex was found to contain approximately 11 molecules of ADP and of ³²P per dodecamer using [γ-³²P]ATP. Reactivation of the inactive enzyme complex was achieved by incubating the enzyme complex in 50 mm acetate (pH 4.4), 1 m KCl, and 0.40 m (NH₄)₂SO₄. ADP, phosphinothricin, and P_i were released upon reactivation.