Energy Charge and Protein Synthesis

Biosynthesis of Histidine

The biosynthesis of histidine in Escherichia coli and Salmonella typhimurium has been an important model system for the study of relationships between the flow of intermediates through a biosynthetic pathway and the control of the genes encoding the enzymes that catalyze the steps in a pathway. This article provides a comprehensive review of the histidine biosynthetic pathway and enzymes, including regulation of the flow of intermediates through the pathway and mechanisms that regulate the amounts of the histidine biosynthetic enzymes. In addition, this article reviews the structure and regulation of the histidine (his) biosynthetic operon, including transcript processing, Rho-factor-dependent "classical" polarity, and the current model of his operon attenuation control. Emphasis is placed on areas of recent progress. Notably, most of the enzymes that catalyze histidine biosynthesis have recently been crystallized, and their structures have been determined. Many of the histidine biosynthetic intermediates are unstable, and the histidine biosynthetic enzymes catalyze some chemically unusual reactions. Therefore, these studies have led to considerable mechanistic insight into the pathway itself and have provided deep biochemical understanding of several fundamental processes, such as feedback control, allosteric interactions, and metabolite channeling. Considerable recent progress has also been made on aspects of his operon regulation, including the mechanism of pp(p)Gpp stimulation of his operon transcription, the molecular basis for transcriptional pausing by RNA polymerase, and pathway evolution. The progress in these areas will continue as sophisticated new genomic, metabolomic, proteomic, and structural approaches converge in studies of the histidine biosynthetic pathway and mechanisms of control of his biosynthetic genes in other bacterial species.

Catalysis of tRNA aminoacylation: single turnover to steady-state kinetics of tRNA synthetases

Aminoacyl-tRNA synthetases (aaRS) catalyze the bimolecular association reaction between amino acid and tRNA by specifically and unerringly choosing the cognate amino acid and tRNA. There are two classes of such synthetases that perform tRNA-aminoacylation reaction. Interestingly, these two classes of aminoacyl-tRNA synthetases differ not only in their structures but they also exhibit remarkably distinct kinetics under pre-steady-state condition. The class I synthetases show initial burst of product formation followed by a slower steady-state rate. This has been argued to represent the influence of slow product release. In contrast, there is no burst in the case of class II enzymes. The tight binding of product with enzyme for class I enzymes is correlated with the enhancement of rate in presence of elongation factor EF-TU. In spite of extensive experimental studies, there is no detailed theoretical analysis that can provide a quantitative understanding of this important problem. In this article, we present a theoretical investigation of enzyme kinetics for both classes of aminoacyl-tRNA synthetases. We present an augmented kinetic scheme and then employ the methods of time-dependent probability statistics to obtain expressions for the first passage time distribution that gives both the time-dependent and the steady-state rates. The present study quantitatively explains all the above experimental observations. We propose an alternative path way in the case of class II enzymes showing the tRNA-dependent amino acid activation and the discrepancy between the single-turnover and steady-state rate.

A substrate-assisted concerted mechanism for aminoacylation by a class II aminoacyl-tRNA synthetase

Aminoacyl-tRNA synthetases (aaRS) join amino acids to their cognate transfer RNAs, establishing an essential coding relationship in translation. To investigate the mechanism of aminoacyl transfer in class II Escherichia coli histidyl-tRNA synthetase (HisRS), we devised a rapid quench assay. Under single turnover conditions with limiting tRNA, aminoacyl transfer proceeds at 18.8 s(-)(1), whereas in the steady state, the overall rate of aminoacylation is limited by amino acid activation to a rate of 3 s(-)(1). In vivo, this mechanism may serve to allow the size of amino acid pools and energy charge to control the rate of aminoacylation and thus protein synthesis. Aminoacyl transfer experiments using HisRS active site mutants and phosphorothioate-substituted adenylate showed that substitution of the nonbridging Sp oxygen of the adenylate decreased the transfer rate at least 10 000-fold, providing direct experimental evidence for the role of this group as a general base for the reaction. Other kinetic experiments revealed that the rate of aminoacyl transfer is independent of the interaction between the carboxyamide group of Gln127 and the alpha-carboxylate carbon, arguing against the formation of a tetrahedral intermediate during the aminoacyl transfer. These experiments support a substrate-assisted concerted mechanism for HisRS, a feature that may generalize to other aaRS, as well as the peptidyl transferase center.

Enhanced levels of cyclic AMP, adenosine(5')tetraphospho(5')adenosine and nucleoside 5'-triphosphates in mouse leukemia P388/D1 after treatment with cis-diamminedichloroplatinum(II)

As part of the exploration of the mechanism of platinum(II) complex-induced growth inhibition and/or cytotoxicity, we studied the intracellular levels of several nucleotides during treatment of mouse leukemia P388/D1 at selected concentrations of 1 microM cis-diamminedichloroplatinum(II) (cis-DDP) and 20 microM of its trans-isomer (trans-DDP). The effects and their time-dependences are correlated with those on cell growth parameters previously published (Just G and Holler E, Cancer Res 49: 7072-7078, 1989). The effects of cis-DDP are strong and irreversible, whereas those of trans-DDP are marginal and reversible, in parallel with similar effects on cell growth parameters. Concentrations of nucleoside 5'-di- and 5'-triphosphates increase in parallel with cellular DNA and protein content by three- to four-fold after 60 hr of treatment. The nucleoside monophosphates dAMP, dGMP and dTMP reveal concentration maxima during exponential cell growth that are two- to six-fold higher than in the control cultures. Levels of cyclic AMP, adenosine(5')tetraphospho(5')adenosine (Ap4A) and CDP rise three- to five-fold above those in the control cultures within a few hours of the start of treatment. The level of coenzyme NAD+ falls below that of the control, concomitantly with an arrest of cells in the G2 phase of the cell cycle and with the appearance of giant cells. Due to the high reactivity of cis-DDP and the continuous concentration increase during the treatment, purine nucleoside 5'-triphosphates provide a possibility for the acquisition of resistance to cis-DDP. The correlation of responses of metabolically and regulatory active nucleotides with biological effects suggests their function in antitumorigenesis.

Effects of succinate on amino acid incorporation into protein during chemical carcinogenesis

The starting point of this study is the observation that succinate, the well-known Krebs cycle intermediate, strongly inhibits the incorporation of amino acids into protein of tissue slices. The results presented in this paper show that this somewhat peculiar succinate effect, which is present in regenerating liver and in a well-differentiated hepatoma and absent in two anaplastic hepatomas, is well-marked in all stages of hepatic carcinogenesis by N,N'-dimethyl-4-aminoazobenzene. A working hypothesis is that the inhibition by succinate of the amino acid incorporation into protein is mediated by a shift of the redox level in the cell toward a more reduced condition.

Studies on the regulation of the branched chain amino acyl-tRNA synthetases of the fungusNeurospora crassa

The specific activities of the branched chain amino acyl-tRNA synthetases from the cytosolic and mitochondrial fractions ofN. crassa were low in dormant conidia and increased during germination, reaching a maximum 8 h after inoculation. This stage of development is characterised by high rates of many other cellular activities.The increases in activity of synthetases of both cytosol and mitochondria are inhibited by cycloheximide indicating that they are synthesized on cytoplasmic ribosomes. The mitochondrial synthetases show a stimulation of their specific activity when mitochondrial RNA and protein synthesis are inhibited by either ethidium bromide or chloramphenicol suggesting that a mitochondrial translation product regulates the synthesis of the mitochondrial synthetases.The activities of amino acyl-tRNA synthetases are dependent on energy production. When respiration is uncoupled from oxidative phosphorylation, synthetase specific activities decrease although the activities of other mitochondrial enzymes like NADH-dehydrogenase increase. This phenomenon suggests that more than one mechanism regulates the synthesis of mitochondrial proteins which are formed on cytoplasmic ribosomes.The synthesis of branched chain amino acyl-tRNA synthetases ofNeurospora is neither repressed by their cognate amino acids, nor is there inhibition by the precursors of these amino acids, as has been observed in other amino acyl-tRNA synthetases of various organism includingNeurospora.

Structural and physiological studies of the Escherichia coli histidine operon inserted into plasmid vectors

A fragment of deoxyribonucleic acid 5,300 base paris long and containing the promoter-proximal portion of the histidine operon of Escherichia coli K-12, has been cloned in plasmid pBR313 (plasmids pCB2 and pCB3). Restriction mapping, partial nucleotide sequencing, and studies on functional expression in vivo and on protein synthesis in minicells have shown that the fragment contains the regulatory region of the operon, the hisG, hisD genes, and part of the hisC gene. Another plasmid (pCB5) contained the hisG gene and part of the hisD gene. Expression of the hisG gene in the latter plasmid was under control of the tetracycline promoter of the pBR313 plasmid. The in vivo expression of the two groups of plasmids described above, as well as their effect on the expression of the histidine genes not carried by the plasmids but present on the host chromosome, has been studied. The presence of multiple copies of pCB2 or pCB3, but not of pCB5, prevented derepression of the chromosomal histidine operon. Possible interpretations of this phenomenon are discussed.

Arginyl-transfer ribonucleic acid synthetase of Bacillus stearothermophilus. Purification and kinetic analysis

Arginyl-tRNA synthetase from Bacillus stearothermophilus (NCA 1518) has been purified 880-fold to apparent homogeneity as demonstrated by electrophoresis in the presence of sodium dodecyl sulphate. The molecular weight is 59 000 as confirmed by Sephadex G-100 and by sucrose gradient ultracentrifugation. The enzyme is monomeric, no subunits were detected. Its cognate tRNA induces an apparent increase in molecular weight suggesting the dimerisation of the enzyme. Nevertheless, it is not obvious that the enzyme dimer forms prior to the aminoacylation reaction catalysed by the enzyme. An ATPase activity was found associated to the synthetase but can be neglected because the ATP consumption is too low for hampering the arginyl-tRNA synthetase activity. The order of addition of substrates and release of products has been studied by measurements of initial velocity, product inhibition and dead-end inhibition. The nature of the kinetic patterns indicates that the aminoacylation reaction conforms to the classical concept of the mechanism which includes the formation of an enzyme-bound aminoacyl-adenylate as an intermediate in the first step followed by transfer of the amino acid to tRNA. The first partial reaction, measured by the ATP-32PPi exchange or AMP synthesis in the presence of ATP and arginine, requires tRNA, which is consistent with the model in which tRNAArg is an activator of the arginyladenylate synthesis.

Phenobarbitone-induced stimulation of protein synthesis in liver of diabetic rat

The effect of phenobarbitone on liver weight, on the rate of protein synthesis and on the sedimentation profiles of polyribosomes from livers was studied in diabetic rats. The rate of protein synthesis by isolated postmitochondrial supernatants from diabetic rats is lower than that from normal animals. The analysis of polyribosome profiles and the effect of Sephadex chromatography on protein synthesis demonstrated that the reduction was dependent in part on polyribosomal disaggregation and in part on the presence in the cytosol of low molecular weight inhibitor(s). Phenobarbitone administration had the same effect in either diabetic or normal rats in that it increased, (a) the degree of polyribosomal aggregation, (b) the rate of protein synthesis by the isolated postmitochondrial supernatants, (c) liver weight and (d) the activity of the inducible enzyme, NADPH-cytochrome c reductase. Both polyribosomal and soluble factors appear to be involved in the phenobarbitone effect. As the diabetic rats do not secret insulin the results suggest that insulin is not involved in the control of protein synthesis by phenobarbitone. It is suggested that the intracellular redox state has a major influence on the rate of protein synthesis.

Histidyl transfer ribonucleic acid synthetase from Salmonella typhimurium. Interaction with substrates and ATP analogues

Structural requirements for substrate binding to histidyl-tRNA synthetase from Salmonella typhimurium have been investigated using ATP analogues. Ki values and the relative binding affinity of the enzyme for these analogues have been determined in the tRNA aminoacylation reaction. The enzyme is highly specific for ATP: no binding was found for GTP, CTP, TTP and UTP. dATP is a very poor substrate for acylation of tRNA, with a Km 40-fold higher than that of ATP. Binding of adenosine 5'-triphosphate requires interactions of the amino group of adenosine and the sugar moiety; the 2' and the 5' positions of the ribose appear to be essential for recognition; the phosphate groups enhance the binding. AMP is a noncompetitive inhibitor with ATP. The interaction of histidyl-tRNA synthetase, a dimeric enzyme, with histidine and ATP was examined by fluorescence measurements at equilibrium and by equilibrium dialysis. Binding with L-histidine is significantly tighter at pH 6 than at pH 7, while the ATP binding is independent of pH. The stoichiometry was measured at pH 6 than at pH 7, while the ATP binding is independent of pH. The stoichiometry was measured at pH 7.5 by equilibrium dialysis and is 1 mol ATP/mol enzyme and, variably, close to 2 or 1 mol histidine/mol enzyme.

Histidyl-tRNA synthetase from Salmonella typhimurium: specificity in the binding of histidine analogues

The topography of the active site of histidyl-tRNA synthetase has been investigated by determining Ki values for a variety of structural analogues of histidine, using the ATP-PPi exchange and tRNA aminoacylation reactions. Using these kinetic constants it has been possible to have a measure of the relative binding affinity of the enzyme for the histidine analogues. The following conclusions have been drawn: (a) the enzyme is stereospecific in the formation of aminoacyl-tRNA complexes, since the D-isomer of histidine does not influence the two reactions; (b) the carboxyl group is not required for binding; (c) bulky derivatives of the carboxyl group prevent the molecules from binding to the enzyme; (d) the amino group permits a good binding affinity; (e) the length of the ring side chain plays a very important role as point of attachment to the enzyme; (f) the kinds of heteroatoms on the ring determine the inhibitory properties of the analogues.

Regulation of bacterial growth

Is the control of bacterial metabolism so complex? The answer can be found in a simple experiment. Two cultures of bacteria are grown in different mediums. One contains as the carbon and nitrogen sources a mixture of amino acids, while the other contains only glucose and ammonia, so that the cells must synthesize all of the amino acids. The results show that insofar as the cells in both cultures grow at comparable rates, they will have the same composition in terms of DNA, RNA, and protein (30). To explain this phenomena I have argued that through the control mechanisms responsible for the distribution of substrates in intermediary metabolism, the substrates of protein synthesis are produced at concentrations and rates commensurate with the ability of the environment to support growth. The provision of these substrates relative to the ability of the protein forming system to utilize them regulates the synthesis of ribosomal and transfer RNA, which, after adjustment for various modulating influences, such as nonfunctioning ribosomes or ribosomal RNA turnover, brings the number of functioning ribosomes to a point in keeping with the provision of external nutrients. The synthesis of messenger (or total) RNA, ribosomal proteins, and DNA, and the process of cell division, for example, are subject to their own controls, but through the burden they each place on intermediary metabolism, they provide a means for partitioning the cell's metabolic resources. It might be noted that this view may not be very far from the idea once held that the rate at which each of the transfer RNA's was changed by amino acids regulate the synthesis of bacterial RNA, but growth regulation is clearly more complicated than implied by that model (76).

Percent charging of transfer ribonucleic acid and levels of ppGpp and pppGpp in dormant and germinated spores of Bacillus megaterium

The levels of transfer ribonucleic acids (tRNAs) specific for 14 amino acids were almost identical in dormant spores and in spores germinated from 6 to 75 min. Germinated spore tRNAs specific for all amino acids tested were between 63 and 93% charged, and there was no significant change in this value from 6 to 75 min of germination. In contrast, tRNAs isolated from dormant spores specific for nine different amino acids were almost completely(>93%) uncharged. However, some dormant spore tRNAs, i.e., those for arginine, histidine, isoleucine, and valine, showed significant (21 to 72%) levels of aminoacylation. Dormant spores contained no detectable guanosine penta- (pppGpp), tetra- (ppGpp), or triphosphate (GTP). However, these nucleotides appeared in the first minutes of germination, and thereafter all increased in parallel with a ratio of pppGpp plus ppGpp to GTP of 0.07 to 0.11, which is characteristic of unstarved vegetative cells.

Regulation at the phosphoenolpyruvate branchpoint in Azotobacter vinelandii: phosphoenolpyruvate carboxylase

Phosphoenolpyruvate carboxylase (EC 4.1.1.31) from Azotobacter vinelandii, like the corresponding enzyme from other organisms, is activated by acetyl coenzyme A and inhibited by l-aspartate. Both modifiers affect primarily the affinity of the enzyme for phosphoenolpyruvate. This is the first enzyme with a strictly anaplerotic (intermediate-replacing) function to be tested for response to the adenylate energy charge; it is entirely insensitive to variation in charge. The results suggest that carboxylation of phosphoenolpyruvate in this organism is controlled by negative feedback from aspartate and by the stimulatory effect of acetyl coenzyme A. The adenylate energy charge may be expected to affect the rate of this reaction indirectly through its effects on the concentrations of acetyl coenzyme A and l-aspartate.