Regulatory Mechanisms Involving Nicotinamide Adenine Nucleotides as Allosteric Effectors

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP

Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was recently discovered to function as a biological hydrotrope. Here, we use mass spectrometry to interrogate ATP-mediated regulation of protein thermal stability and protein solubility on a proteome-wide scale. Thermal proteome profiling reveals high affinity interactions of ATP as a substrate and as an allosteric modulator that has widespread influence on protein complexes and their stability. Further, we develop a strategy for proteome-wide solubility profiling, and discover ATP-dependent solubilization of at least 25% of the insoluble proteome. ATP increases the solubility of positively charged, intrinsically disordered proteins, and their susceptibility for solubilization varies depending on their localization to different membrane-less organelles. Moreover, a few proteins, exhibit an ATP-dependent decrease in solubility, likely reflecting polymer formation. Our data provides a proteome-wide, quantitative insight into how ATP influences protein structure and solubility across the spectrum of physiologically relevant concentrations.

ATP can function as a biological hydrotrope, but its global effects on protein solubility have not yet been characterized. Here, the authors quantify the effect of ATP on the thermal stability and solubility of the cellular proteome, providing insights into protein solubility regulation by ATP.

Microaerophilic bacteria transduce energy via oxidative metabolic gearing

Heterotrophic microaerophilic bacteria, a diverse and ubiquitous group, are specialized for growth in O2 limited environments. Until recently, microaerophilic bacteria have been grouped with obligate aerobic organisms whose metabolic rates slow in response to physiological O2 limitation. In contrast, microaerophilic bacteria are adapted to maintain essentially constant turnover of primary energy substrates in response to a wide range of physiological O2. This capacity, oxidative metabolic gearing, allows microaerophilic bacteria to maintain catabolic enzymes, substrates, and cofactors at high steady-state levels. Oxidative metabolic gearing is thus adaptive, as it allows microaerophilic bacteria to respond to changes in physiological O2 relatively rapidly when compared to aerobic, anaerobic, or facultative microorganisms.

Flux through citrate synthase limits the growth of ethanologenic Escherichia coli KO11 during xylose fermentation

Previous studies have shown that high levels of complex nutrients (Luria broth or 5% corn steep liquor) were necessary for rapid ethanol production by the ethanologenic strain Escherichia coli KO11. Although this strain is prototrophic, cell density and ethanol production remained low in mineral salts media (10% xylose) unless complex nutrients were added. The basis for this nutrient requirement was identified as a regulatory problem created by metabolic engineering of an ethanol pathway. Cells must partition pyruvate between competing needs for biosynthesis and regeneration of NAD(+). Expression of low-K(m) Zymomonas mobilis pdc (pyruvate decarboxylase) in KO11 reduced the flow of pyruvate carbon into native fermentation pathways as desired, but it also restricted the flow of carbon skeletons into the 2-ketoglutarate arm of the tricarboxylic acid pathway (biosynthesis). In mineral salts medium containing 1% corn steep liquor and 10% xylose, the detrimental effect of metabolic engineering was substantially reduced by addition of pyruvate. A similar benefit was also observed when acetaldehyde, 2-ketoglutarate, or glutamate was added. In E. coli, citrate synthase links the cellular abundance of NADH to the supply of 2-ketoglutarate for glutamate biosynthesis. This enzyme is allosterically regulated and inhibited by high NADH concentrations. In addition, citrate synthase catalyzes the first committed step in 2-ketoglutarate synthesis. Oxidation of NADH by added acetaldehyde (or pyruvate) would be expected to increase the activity of E. coli citrate synthase and direct more carbon into 2-ketoglutarate, and this may explain the stimulation of growth. This hypothesis was tested, in part, by cloning the Bacillus subtilis citZ gene encoding an NADH-insensitive citrate synthase. Expression of recombinant citZ in KO11 was accompanied by increases in cell growth and ethanol production, which substantially reduced the need for complex nutrients.

Azorhizobium caulinodans pyruvate dehydrogenase activity is dispensable for aerobic but required for microaerobic growth

Azorhizobium caulinodans mutant 62004 carries a null allele of pdhB, encoding the E1beta subunit of pyruvate dehydrogenase, which converts pyruvate to acetyl-CoA. This pdhB mutant completely lacks pyruvate oxidation activities yet grows aerobically on C(4) dicarboxylates (succinate, L-malate) as sole energy source, albeit slowly, and displays pleiotropic growth defects consistent with physiological acetyl-CoA limitation. Temperature-sensitive (ts), conditional-lethal derivatives of the pdhB mutant lack (methyl)malonate semialdehyde dehydrogenase activity, which thus also allows L-malate conversion to acetyl-CoA. The pdhB mutant remains able to fix N(2) in aerobic culture, but is unable to fix N(2) in symbiosis with host Sesbania rostrata plants and cannot grow microaerobically. In culture, A. caulinodans wild-type can use acetate, beta-D-hydroxybutyrate and nicotinate--all direct precursors of acetyl-CoA--as sole C and energy source for aerobic, but not microaerobic growth. Paradoxically, acetyl-CoA is thus a required intermediate for microaerobic oxidative energy transduction while not itself oxidized. Accordingly, A. caulinodans energy transduction under aerobic and microaerobic conditions is qualitatively different.

Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli

Oxidation of malate to oxaloacetate in Escherichia coli can be catalyzed by two enzymes: the well-known NAD-dependent malate dehydrogenase (MDH; EC 1.1.1.37) and the membrane-associated malate:quinone-oxidoreductase (MQO; EC 1.1.99.16), encoded by the gene mqo (previously called yojH). Expression of the mqo gene and, consequently, MQO activity are regulated by carbon and energy source for growth. In batch cultures, MQO activity was highest during exponential growth and decreased sharply after onset of the stationary phase. Experiments with the beta-galactosidase reporter fused to the promoter of the mqo gene indicate that its transcription is regulated by the ArcA-ArcB two-component system. In contrast to earlier reports, MDH did not repress mqo expression. On the contrary, MQO and MDH are active at the same time in E. coli. For Corynebacterium glutamicum, it was found that MQO is the principal enzyme catalyzing the oxidation of malate to oxaloacetate. These observations justified a reinvestigation of the roles of MDH and MQO in the citric acid cycle of E. coli. In this organism, a defined deletion of the mdh gene led to severely decreased rates of growth on several substrates. Deletion of the mqo gene did not produce a distinguishable effect on the growth rate, nor did it affect the fitness of the organism in competition with the wild type. To investigate whether in an mqo mutant the conversion of malate to oxaloacetate could have been taken over by a bypass route via malic enzyme, phosphoenolpyruvate synthase, and phosphenolpyruvate carboxylase, deletion mutants of the malic enzyme genes sfcA and b2463 (coding for EC 1.1.1.38 and EC 1.1.1.40, respectively) and of the phosphoenolpyruvate synthase (EC 2.7.9.2) gene pps were created. They were introduced separately or together with the deletion of mqo. These studies did not reveal a significant role for MQO in malate oxidation in wild-type E. coli. However, comparing growth of the mdh single mutant to that of the double mutant containing mdh and mqo deletions did indicate that MQO partly takes over the function of MDH in an mdh mutant.

Crystalline NAD/NADP-dependent malate dehydrogenase; the enzyme from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius

Malate dehydrogenase from Sulfolobus acidocaldarius has been purified 240-fold to apparent electrophoretic homogeneity. The enzyme shows a specific activity of 277 U/mg and crystallizes readily. The relative molecular mass of the native enzyme is estimated as 128,500 by ultracentrifugation. After cross-linking a relative molecular mass of 134,000 is found by sodium dodecyl sulfate gel electrophoresis. Malate dehydrogenase from S. acidocaldarius is composed of four subunits of identical size with a relative molecular mass of 34,000. Active-enzyme sedimentation in the analytical ultracentrifuge indicates that the tetramer is the catalytically active species. Kinetic studies in the direction of oxaloacetate reduction showed a Km for NADH of 4.1 microM and a Km for oxaloacetate of 52 microM. Oxaloacetate exhibits substrate inhibition at higher concentrations, L-malate, NAD and NADP were found to be product inhibitors. The enzymatic activity is inhibited by 2-oxoglutarate but not by the adenosine nucleotides AMP, ADP and ATP. Only low activity is detected in the direction of malate oxidation. Malate dehydrogenase from S. acidocaldarius utilizes both NADH and NADPH to reduce oxaloacetate. The enzyme shows A-side stereospecificity for both nicotinamide dinucleotides.

Negative modulation of Escherichia coli NAD kinase by NADPH and NADH

NAD kinase was purified 93-fold from Escherichia coli. The enzyme was found to have a pH optimum of 7.2 and an apparent Km for NAD+, ATP, and Mg2+ of 1.9, 2.1, and 4.1 mM, respectively. Several compounds including quinolinic acid, nicotinic acid, nicotinamide, nicotinamide mononucleotide, AMP, ADP, and NADP+ did not affect NAD kinase activity. The enzyme was not affected by changes in the adenylate energy charge. In contrast, both NADH and NADPH were potent negative modulators of the enzyme, since their presence at micromolar concentrations resulted in a pronounced sigmoidal NAD+ saturation curve. In addition, the presence of a range of concentrations of the reduced nucleotides resulted in an increase of the Hill slope (nH) to 1.7 to 2.0 with NADH and to 1.8 to 2.1 with NADPH, suggesting that NAD kinase is an allosteric enzyme. These results indicate that NAD kinase activity is regulated by the availability of ATP, NAD+, and Mg2+ and, more significantly, by changes in the NADP+/NADPH and NAD+/NADH ratios. Thus, NAD kinase probably plays a role in the regulation of NADP turnover and pool size in E. coli.

The effects of cadmium on succinate and NADH-linked substrate oxidations in rat hepatic mitochondria

Low concentrations of cadmium (3.3-40 microM) inhibited State 3 NADH-linked respiration in rat hepatic mitochondria, but failed to release oligomycin (1 microgram) inhibited State 3 respiration, or to significantly change the State 4 rate. In the presence of succinate, 40 microM cadmium inhibited State 3 respiration by 89%, while concentrations between 3.3 and 13.3 microM stimulated State 4 respiration. Higher concentrations caused marked inhibition. In the presence of succinate, cadmium released oligomycin inhibited State 3 respiration. Cadmium (0.001-1.0 mM) did not stimulate mitochondrial ATPase activity or inhibit ferricyanide reduction, but stimulated NAD+ linked mitochondrial dehydrogenase activities and NADH oxidation. These results indicate that cadmium interacts with either the NADH dehydrogenase complex or other NADH-dependent enzymes and not solely by an uncoupling action.

Metabolism of L-fucose and L-rhamnose in Escherichia coli: differences in induction of propanediol oxidoreductase

Escherichia coli is capable of growing on L-fucose or L-rhamnose as a sole source of carbon and energy. When grown under anaerobic conditions on either sugar, a nicotinamide adenine dinucleotide-linked L-lactaldehyde:propanediol oxidoreductase activity is induced. The functioning of this enzyme results in the regeneration of oxidized nicotinamide adenine dinucleotide. Conditions of induction of the enzyme activity were studied and were found to display different characteristics on each sugar. In the rhamnose-grown cells, the increase in enzyme activity detected under inducing conditions was accompanied by the synthesis of propanediol oxidoreductase, as measured by the appearance in the extracts of a protein that reacts with propanediol oxidoreductase antibodies. In contrast, in fucose-grown cells, the level of propanediol oxidoreductase as measured by enzyme antibody-reacting material was high under noninducing and inducing conditions. Thus, the increase in enzyme activity detected in going from noninducing to inducing conditions in fucose-grown cells did not depend on the appearance of the specific protein but on the activation of the propanediol oxidoreductase already present in the cells in an inactive form. The propanediol oxidoreductase of both homologous systems should consequently be regulated by different control mechanisms.

Genetic and physiological characterization of Escherichia coli mutants deficient in phosphoenolpyruvate carboxykinase activity

Mutants doubly deficient in phosphoenolpyruvate carboxykinase (pck) and phosphoenolpyruvate synthetase (pps) were unable to grow with succinate as the sole carbon source. A number of pck mutations isolated from pps strains by penicillin selection mapped at 74 min on the Escherichia coli chromosome, between glpD and aroB. Several of the strains containing these mutations had a protein antigenically related to phosphoenolpyruvate carboxykinase, and therefore, the mutations probably represented mutations in the structural gene for this enzyme. Phosphoenolpyruvate carboxykinase was regulated at the level of transcription by catabolite repression. Enzyme levels also increased in stationary-phase cultures by a mechanism independent of cyclic adenosine monophosphate or the product of the relA gene.

Streptococcal extracellular NAD+ nucleosidase. Characterization of changes occurring during purification

Purification of streptococcal extracellular NAD+ nucleosidase is associated with changes of kinetic properties. A high-molecular weight component is required for a full activity of the enzyme. The component is not produced by bacteria and is present in the Todd-Hewitt cultivation medium, the beef-heart extract serving primarily as its source. In its effect on the enzyme this component can be replaced with bovine albumin. It follows from the time relationship of the NAD decomposition that the mechanism of the studied enzymic reaction is not hydrolytic. In addition to nicotinamide, a product of polymeric character is formed.

The molecular mechanism of dicarboxylic acid transport in Escherichia coli K 12

It is the purpose of this communication to review the properties of the dicarboxylic acid transport system in Escherichia coli K 12, in particular the role of various dicarboxylate transport proteins, and the disposition of these components in the cytoplasmic membrane. The dicarboxylate transport system is an active process and is responsible for the uptake of succinate, fumarate, and malate. Membrane vesicles prepared from the EDTA, lysozyme, and osmotic shock treatment take up the dicarboxylic acids in the presence of an electron donor. Genetic analysis of various transport mutants indicates that there is only one dicarboxylic acid transport system present in Escherichia coli K 12, and that at least 3 genes, designated cbt, dct A, and dct B, are involved in this transport system. The products corresponding to the 3 genes are: a periplasmic binding protein (PBP) specified by cbt, and 2 membrane integral proteins, SBP 1 and SBP 2, specified by dct B and dct A, respectively. Components SBP 1 and SBP 2 appear to be exposed on both the inner and outer surfaces of the membrane, and lie in close proximity to each other. The substrate recognition sites of SBP 2 and SBP 1 are exposed on the outer and inner surfaces of the membrane respectively. The data presently available suggest that dicarboxylic acids may be translocated across the membrane via a transport channel. A tentative working model on the mechanism of translocation of dicarboxylic acids across the cell envelope by the periplasmic binding protein, and the 2 membrane carrier proteins is presented.

[Inducible accumulation of alpha-ketoglutaric acid in cultures of Streptomyces hygroscopicus JA 6599 producing a macrolide antibiotic]

The excessive production of pyruvic and 2-oxoglutaric acid by S. hygroscopicus JA 6599 grown on a medium rich in complex carbon and nitrogen sources was studied. Towards the end of the first day of batch cultivation a maximum level of both keto acids in the medium was observed. By diluting the complete culture with water at 22nd hour, however, a further increase in 2-oxoglutarate concentration was induced and the antibiotic production was slightly stimulated. In diluted cultures the oxygen saturation was found to be distinctly higher than in non-diluted ones and, on the other hand, the mycelial activities of both pyruvate and 2-oxoglutarate decarboxylases were decreased. Since the 2-oxoglutarate level was strongly influenced by inhibitors of glycolysis and of citric acid cycle, it is suggested that the metabolite accumulation in diluted cultures is mainly caused by modifications of the metabolic control of carbohydrate catabolism due to an improved aeration. Furthermore, the macrolide antibiotic A 6599 produced by S. hygroscopicus JA 6599 itself was shown to interfere with the accumulation of 2-oxoglutaric acid.