Cloning of the tyrocidine synthetase 1 gene from Bacillus brevis and its expression in Escherichia coli

Summary The entire structural gene for tyrocidine synthetase 1 from Bacillus brevis ATCC 8185 has been cloned and expressed in Escherichia coli. Transformed E. coli cells were screened for their ability to produce tyrocidine synthetase 1 by in situ immunoassay using antibodies against gramicidin S synthetase 2 which cross-react with tyrocidine synthetase 1. The cloned gene is within a 5.2 kb fragment of B. brevis genomic DNA and requires no external promoter for its expression in E. coli. It was also observed that cloning of the 5.2 kb insert in the opposite orientation still resulted in a high level of tyrocidine synthetase 1 expression in transformed E. coli cells. In addition, protein blotting and partial purification of the gene product by gel filtration revealed a major protein of molecular weight about 100,000 with specific d-phenylalanine dependent ATP-³²PP_i and 2deoxy ATP-³²PP_i exchange activities. These unique activities of tyrocidine synthetase 1 were not detected in protein extracts of E. coli strains carrying the vector.     

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.     

Effect of lysolecithin treatment on the structure and functions of the mitochondrial inner membrane

Lysolecithin treatment of electron transport particles (ETP) generated membrane fragments capable of catalyzing ATP-³²P_i exchange, which was resistant to the uncoupling action of Valinomycin plus Nigericin or Valinomycin plus Monensin A in the presence of K⁺. Electron micrographs of ultrathin, positively stained sections of lysolecithin treated ETP were virtually devoid of circular patterns characteristic of closed vesicles. The results suggest that the closed vesicular structure of the mitochondrial inner membrane demanded by the chemiosmotic hypothesis of energy transduction (1) may not be essential for the ATP-³²P_i exchange reaction.     

32P-labeling of bovine tryptophanyl-tRNA synthetase with [32P]pyrophosphate

The covalent derivative of the tryptophanyl-tRNA synthetase obtained under the action of³²PP_i contains one mole of the covalently bound pyrophosphate (or 2 moles of orthophosphate) per mole of dimeric enzyme. Dephosphorylation with alkaline phosphatase causes practically no changes of enzymatic activity although the enzyme looses its ability to bind PP_i.Enzymes tryptophanyl-tRNA synthetase (EC 6.1.1.2), alkaline phosphatase (EC 3.1.3.1), inorganic pyrophosphatase (EC 3.6.1.1)     

Reconstitution of ATP-32-Pi exchange by phospholipid addition to the purified oligomycin-sensitive ATPase from yeast mitochondria.

A purified preparation of the oligomycin-sensitive ATPase from yeast mitochondria has been shown to elicit ATP-³²P_i exchange when combined with phospholipids. The reconstitution was normally carried out by dialysis of an ATPase-phospholipid-bile detergent mixture, but could also be achieved by direct addition of the lipid. Vesicle structures with diameters between 200 and 1500 Å were seen by electron microscopy.The ATP-³²P_i exchange was independent of electron transport but sensitive to uncouplers and energy-transfer inhibitors. As in mitochondria, ATPase activity in the reconstituted system was stimulated by a range of uncouplers which inhibited ATP-³²P_i exchange. Taken together, the results raise the possibility that the terminal coupling mechanism might still be intact within the ATPase complex.     

Studies of the oligomycin-sensitive ATPase from yeast mitochondria. Reconstitution of ATP-32Pi exchange in the presence of phospholipids

A purified preparation of the oligomycin-sensitive ATPase from yeast mitochondria has been shown to elicit an oligomycin- and uncoupler-sensitive ATP-³²P_i exchange in the presence of phospholipids. Reconstitution was normally achieved by dialysis of an ATPase-phospholipid-cholate mixture. Following this procedure, vesicles with diameters between 200 and 1,500 Å were seen by electron microscopy. As in mitochondria, ATPase activity in the reconstituted system was stimulated by a range of uncouplers which inhibited ATP-³²P_i exchange. These and other findings suggest that the coupling mechanism may still be intact within the ATPase complex.     

Purification and reversible subunit dissociation of overproduced Escherichia coli phenylalanyl-tRNA synthetase

Phenylalanyl-tRNA synthetase (EC 6.1.1.20) has been purified to homogeneity from a 100-fold overproducing Escherichia coli strain carrying a hybrid pBR322 plasmid containing the pheS-pheT locus. The purified enzyme is identical to the phenylalanyl-tRNA synthetase isolated from an haploid strain. The enzyme was found to dissociate in the presence of 0.5 M NaSCN and the α- and β-subunits composing the native α₂β₂ enzyme were separated by gel filtration. Neither isolated subunit showed significant catalytic activity. A complex indistinguishable from the native enzyme with full catalytic activity is recovered upon mixing the subunits. The N- and C-terminal sequences and the amino acid composition of each subunit were determined. They are compared to the available data concerning the primary structure of the subunits, as deduced from nucleotide sequencing of the pheS-pheT operon.     

Energy-linked activities in reconstituted yeast adenosine triphosphatase proteoliposome. Adenosine triphosphate formation coupled with electron flow between ascorbate and ferricyanide.

(1) Conditions are described wherein the yeast oligomycin-sensitive adenosine triphosphatase (ATPase) complex can be reconstituted together with phospholipids to yield extremely high rates of ATP-³²P_j exchange. The vesicles so formed exhibit proton uptake upon addition of Mg²⁺-ATP and a relatively slow decay of the proton gradient. (2) The stimulation of ATP-³²P_i exchange by valinomycin + K⁺ reported previously (Ryrie, I. J. (1975) Arch. Biochem. Biophys. 168, 704–711) is apparently not simply due to a diffusion potential. The findings suggest that an electroimpelled, valinomycin-dependent migration of K⁺ may occur together with the electrogenic movements of protons during ATP hydrolysis and synthesis to establish optimal energized conditions for ATP-³²P_i exchange. (3) An artificial oxidative phosphorylation system in the reconstituted vesicles is described: [³²P]ATP formation from ADP and ³²P_i is shown to be linked with electron flow between external ascorbate and internal ferricyanide where a permeable proton carrier, such as phenazine methosulfate, is used to establish a proton gradient. That the yeast ATPase is capable of net ATP synthesis has also been demonstrated in a light-dependent reaction using ATPase proteoliposomes reconstituted together with bacteriorhodopsin.     

Acetate kinase (pyrophosphate). A fourth pyrophosphate-dependent kinase from Entamoeba histolytica.

An enzyme from Entamoeba histolytica catalyzes the formation of acetyl phosphate and orthophosphate from acetate and inorganic pyrophosphate (PP_i), but it displays much greater activity in the direction of acetate formation. It has been purified 40-fold and separated from interfering enzyme activities by chromatography. Its reaction products have been quantitatively established. ATP cannot replace PP_i as phosphoryl donor in the direction of acetyl phosphate formation nor will any common nucleoside diphosphate replace orthophosphate as phosphoryl acceptor in the direction of acetate formation. The trivial name proposed for the new enzyme is acetate kinase (PP_i).     

Yeast nicotinic acid phosphoribosyltransferase. Studies of reaction paths, phosphoenzyme, and Mg2+ effects.

Initial velocity and ATP-ADP isotope exchange kinetic data on yeast nicotinate phosphoribosyltransferase indicate a sequential steady-state mechanism m which ATP adds first, followed by a random order of addition of the substrates PP-ribose-P and nicotinic acid. Reaction flux through the alternative ping-pong pathway, evidenced first by ATP-ADP isotope exchange in the absence of nicotinic acid and PP-ribose-P substrates, is reduced by low concentrations of either, or both, of these substrates. Both Mg²⁺-complexed and -free PP-ribose-P are enzymatically active. Phosphorylated enzyme, prepared with [γ-³²P]ATP and separated by gel chromatography, retains ³²P_i until incubated with both substrates, PP-ribose-P and nicotinic acid, which completely discharge the ³²P_i.     

Nonribosomal peptide synthetases-evidence for a second ATP-binding site

δ-(l-α-Aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) catalyses, via the protein thiotemplate mechanism, the nonribosomal biosynthesis of the penicillin and cephalosporin precursor tripeptide δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine (ACV). The complete and fully saturated biosynthetic system approaches maximum rate of product generation with increasing ATP concentration. Nonproductive adenylation of ACVS, monitored utilising the ATP–[³²P]PP_i exchange reaction, has revealed substrate inhibition with ATP. The kinetic inhibition pattern provides evidence for the existence of a second nucleotide-binding site with possible implication in the regulatory mechanism. Under suboptimal reaction conditions, in the presence of MgATP^2?, l-Cys and inorganic pyrophosphatase, ACVS forms adenosine(5′)tetraphospho(5′)adenosine (Ap₄A) from the reverse reaction of adenylate formation involving a second ATP molecule. The potential location of the second ATP binding site was deduced from sequence comparisons and molecular visualisation in conjunction to data obtained from biochemical analysis.     

Energy-liked reactions in photosynthetic bacteria. X. Solubilization of the membrane-bound energy-linked inorganic pyrophosphatase of Rhodospirillum rubrum.

The energy-linked membrane-bound inorganic pyrophosphatase of $\text{Rhodospirollum}$$\text{rubrum}$, G-9, has been solubilized with good yield from chromatophores using cholate in the presence of MgCl₂. The enzyme has been partially purified using ammonium sulfate fractionation and gel chromatography. After fractionation the enzyme requires phospholipid for activity. The solubilized enzyme is specific for PP_i and requires Mg²⁺ for activity as has been found for other PP_iases.     

Differential inhibition of Pi-ATP exchange in relation to ATP synthesis and hydrolysis by modification of chloroplast thylakoid membranes with glutaraldehyde

Limited modification of thylakoid membranes with glutaraldehyde inhibits the P_i-ATP exchange reaction much more than ATP synthesis or hydrolysis. More extensive modification of the membranes results in the inhibition of all activities of the ATP synthetase, but does not affect electron transport. Limited modification also does not have much effect on the tight binding of [³H]ADP or the ΔpH supported by ATP hydrolysis. The modification affects the catalytic process itself and not the activation of the latent enzyme. Cross-linking between thylakoid polypeptides is observed only after extensive treatment with glutaraldehyde, while limited modification does not result in cross-linking between polypeptides. The differential inhibition of the P_i-ATP exchange relative to ATP hydrolysis can be explained by the decrease in only one of the kinetic rate constants involved in these reactions. However, the relative insensitivity of photophosphorylation to the modification suggests that different enzyme conformations may participate in phosphorylation (light) and ATP hydrolysis or P_i-ATP exchange (dark).     

A nonradioactive high-throughput assay for screening and characterization of adenylation domains for nonribosomal peptide combinatorial biosynthesis

Adenylation domains are critical enzymes that dictate the identity of the amino acid building blocks to be incorporated during nonribosomal peptide (NRP) biosynthesis. NRPs display a wide range of biological activities and are some of the most important drugs currently used in clinics. Traditionally, activity of adenylation domains has been measured by radioactive ATP-[³²P]pyrophosphate (PP_i) exchange assays. To identify adenylation domains for future combinatorial production of novel NRPs as potential drugs, we report a convenient high-throughput nonradioactive method to measure activity of these enzymes. In our assay, malachite green is used to measure orthophosphate (P_i) concentrations after degradation by inorganic pyrophosphatase of the PP_i released during aminoacyl-AMP formation by action of the adenylation domains. The assay is quantitative, accurate, and robust, and it can be performed in 96- and 384-well plate formats. The performance of our assay was tested by using NcpB-A₄, one of the seven adenylation domains involved in nostocyclopeptide biosynthesis. The kinetics of pyrophosphate release monitored by this method are much slower than those measured by a traditional ATP-[³²P]PP_i exchange assay. This observation indicates that the formation of the adenylated amino acid and its release are the rate-limiting steps during the catalytic turnover.     

The regulation of liver phosphoprotein phosphatase by inorganic pyrophosphate and cobalt.

The preincubation of rat liver crude extracts with ATP caused a 60% inactivation of phosphoprotein phosphatase in 30 min at 30 °C. The presence of Mg²⁺, or cyclic AMP, along with ATP in the preincubation mixture had no effect on the inactivation of phosphatase caused by ATP. The crude liver phosphatase was also inactivated by ADP or PP_i; PP_i being the most potent inactivating metabolite. AMP, adenosine or P_i were without any effect. The effect of ATP or PP_i was completely reversed by cobalt. The cobalt effect was very specific and could not be replaced by several metal ions tested except by Mn²⁺ which was partly active. With the aid of sucrose density gradient studies, it was also shown that PP_icauses an apparent conversion of a 4.1 S form to a 7.8 S form of the enzyme in rat liver extracts. Cobalt, on the other hand, converts the higher 7.8 S form to a lower 4.1 S form of the enzyme. The preincubation of purified rabbit liver phosphoprotein phosphatase with PP_i also caused a complete inactivation of the enzyme in 40 min. The inactivation of the enzyme by PP_i was completely reversed by cobalt. Unlike the apparent interconversion between different molecular forms of the enzyme by PP_i and cobalt in rat liver crude extracts, no such interconversion of purified rabbit liver phosphoprotein phosphatase was observed in the presence of PP_i and cobalt.     

Rapid and selective enzymatic assay for l-methionine based on a pyrophosphate detection system

An enzymatic assay for l-methionine was developed by coupling adenosylmethionine synthetase (AdoMetS) to a pyrophosphate (PP_i) detection system, which was constructed using pyruvate, phosphate dikinase. To expand the use of this assay, the PP_i detection system was embodied as three different forms, which allowed PP_i to be measured by UV, visible, and fluorescent light detectors. The assay system was robust and could tolerate the addition of inorganic phosphate and ATP to the assay mixtures. l-Methionine could be accurately determined by coupling the PP_i detection system and AdoMetS. This AdoMetS coupling assay was highly selective to l-methionine and exhibited no significant activity to other proteinaceous amino acids, ammonia, or urea, unlike conventional enzymatic assays for l-methionine. Spike and recovery tests showed that the AdoMetS assay could accurately and reproducibly determine increases in l-methionine in human plasma samples without any pretreatment to remove proteins and potentially interfering low-molecular-weight molecules. The high selectivity and robustness of the AdoMetS assay provide rapid and high-throughput analysis of l-methionine in various kinds of analytes.     

Discovery of PPi-type Phosphoenolpyruvate Carboxykinase Genes in Eukaryotes and Bacteria

Phosphoenolpyruvate carboxykinase (PEPCK) is one of the pivotal enzymes that regulates the carbon flow of the central metabolism by fixing CO₂ to phosphoenolpyruvate (PEP) to produce oxaloacetate or vice versa. Whereas ATP- and GTP-type PEPCKs have been well studied, and their protein identities are established, inorganic pyrophosphate (PP_i)-type PEPCK (PP_i-PEPCK) is poorly characterized. Despite extensive enzymological studies, its protein identity and encoding gene remain unknown. In this study, PP_i-PEPCK has been identified for the first time from a eukaryotic human parasite, Entamoeba histolytica, by conventional purification and mass spectrometric identification of the native enzyme, followed by demonstration of its enzymatic activity. A homolog of the amebic PP_i-PEPCK from an anaerobic bacterium Propionibacterium freudenreichii subsp. shermanii also exhibited PP_i-PEPCK activity. The primary structure of PP_i-PEPCK has no similarity to the functional homologs ATP/GTP-PEPCKs and PEP carboxylase, strongly suggesting that PP_i-PEPCK arose independently from the other functional homologues and very likely has unique catalytic sites. PP_i-PEPCK homologs were found in a variety of bacteria and some eukaryotes but not in archaea. The molecular identification of this long forgotten enzyme shows us the diversity and functional redundancy of enzymes involved in the central metabolism and can help us to understand the central metabolism more deeply.     

Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNA interaction

This paper focuses on several aspects of the specificity of mutants of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) and tRNA^Gln. Temperature-sensitive mutants located in glnS, the gene for GlnRS, have been described previously. The mutations responsible for the temperature-sensitive phenotype were analyzed, and pseudorevertants of these mutants isolated and characterized. The nature of these mutations is discussed in terms of their location in the three-dimensional structure of the tRNA^Gln: GlnRS complex. In order to characterize the specificity of the aminoacylation reaction, mutant tRNA^Gln species were synthesized with either a 2′-deoxy AMP or 3′-deoxy AMP as their 3′-terminal nucleotide. Subsequent assays for aminoacylation and ATP/PP_i exchange activity established the esterification of glutamine to the 2′-hydroxyl of the terminal adenosine: there is no glutaminylation of the 3′-OH group. This correlates with the classification of GlnRS as a class I aminoacyl-tRNA synthetase. Mutations in tRNA^Gln are discussed which affect the recognition of GlnRS and the current concept of glutamine identity in E coli is reviewed.     

On the mechanism of H+ translocation by mitochondrial H+-ATPase. Studies with chemical modifier of tyrosine residues

In this paper a detailed study of the effect of nitration of tyrosine residues by tetranitromethane on H⁺ conduction and other reactions catalyzed by the H⁺-ATPase complex in phosphorylating submitochondrial particles, uncoupled particles, and the purified complex is presented. Tetranitromethane treatment of submitochondrial particles results in marked inhibition of ATP hydrolysis, ATP-³³P_i exchange, and proton conduction by the H⁺-ATPase complex. These effects are caused by nitration of tyrosine residues of H⁺-ATPase complex as shown by the appearance of the absorption peak at 360 nm (specific for nitrotyrosine formation) and inhibition of ATP hydrolysis and ATP-³³P_i exchange in the complex purified from tetranitromethane-treated particles. H⁺ conduction in phospholipid vesicles inlaid with F₀ is also inhibited by tetranitromethane treatment. These observations indicate that tyrosine residue(s) of F₀ are critically involved in energy-linked proton translocation in the ATP-ase complex.