Modified methods for the determination of carbamyl aspartate

Biodegradability of end-groups of the biocide polyhexamethylene biguanide (PHMB) assessed using model compounds

Polyhexamethylene biguanide (PHMB), a biocide used in a wide variety of disinfection and preservation applications, is a polydisperse mixture in which the end-groups may be any combination of amine, guanidine and cyanoguanidine. Using PHMB model compounds (1,6-diaminohexane; 1,6-diguanidinohexane; 1,6-di(cyanoguanidino)hexane; 4-guanidinobutyric acid), we have determined the biodegradation characteristics of each end-group in several strains of bacteria isolated for their ability to utilise PHMB as a sole source of nitrogen. Bacteria were screened for growth at the expense of each model compound (at non-inhibitory concentrations) as sole nitrogen source. None of the isolated bacteria was capable of utilising a cyanoguanidine end-group as growth substrate, whereas several bacteria were shown to utilise amine or guanidine end-groups. In particular, a strain of Pseudomonas putida was capable of extensive growth with 1,6-diguanidinohexane as a sole nitrogen source, with complete removal of guanidine groups from culture medium within 2 days, and with concomitant formation of unsubstituted urea, which in turn was also utilised by the organism. We conclude that whilst amine and guanidine end-groups in PHMB are likely to be susceptible to biodegradation, cyanoguanidine end-groups are likely to be recalcitrant.

L-canavanine is a time-controlled mechanism-based inhibitor of Pseudomonas aeruginosa arginine deiminase

The mechanism for inhibition of the Pseudomonas aeruginosa arginine deiminase (PaADI) by the arginine analogue l-canavanine was investigated. Inhibition by this substance (kinact = 0.31 +/- 0.03 min-1 and Ki = 1.7 +/- 0.5 mM) is associated with the formation of a modestly stable S-alkylthiouronium intermediate, detected by using kinetic techniques and identified by using electrospray ionization mass spectrometry. The electronic and/or orientation effects, caused by oxygen-for-methylene substitution in l-canavanine, on the rate of enzyme regeneration from the S-alkylthiouronium intermediate could serve as the basis for a strategy for the rational design of new slow substrate inhibitors of ADI.

The aspartate transcarbamoylase-dihydroorotase complex in Deinococcus radiophilus has an active dihydroorotase

Aspartate transcarbamoylase (ATCase) and dihydroorotase (DHOase) catalyse the first two steps unique to pyrimidine synthesis. In many bacteria they form non-covalently bonded complexes. There are two types of DHOase, type I and type II which share a common ancestry. Type I is the more ancient form and is present in the complexes. In recently evolved bacteria the DHOase is defective and its function has been replaced by a type II DHOase which is separate from the complex. Deinococcus radiophilus diverges early on the phylogenetic tree and so might be expected to have an active type I DHOase. Purification of the 500 kDa ATCase-DHOase complex, by conventional techniques, showed it to possess an active DHOase.

Regulation of the Pyrimidine Biosynthetic Pathway in Pseudomonas mucidolens

Control of pyrimidine biosynthesis was examined in Pseudomonas mucidolens ATCC 4685 and the five de novo pyrimidine biosynthetic enzyme activities unique to this pathway were influenced by pyrimidine supplementation in cells grown on glucose or succinate as a carbon source. When uracil was supplemented to glucose-grown ATCC 4685 cells, activities of four de novo enzymes were depressed which indicated possible repression of enzyme synthesis. To learn whether the pathway was repressible, pyrimidine limitation experiments were conducted using an orotate phosphoribosyltransferase (pyrE) mutant strain identified in this study. Compared to excess uracil growth conditions for the glucose-grown mutant strain cells, pyrimidine limitation of this strain caused aspartate transcarbamoylase, dihydroorotase and dihydroorotate dehydrogenase activities to increase by more than 3-fold while OMP decarboxylase activity increased by 2.7-fold. The syntheses of the de novo enzymes appeared to be regulated by pyrimidines. At the level of enzyme activity, aspartate transcarbamoylase activity in P. mucidolens ATCC 4685 was subject to inhibition at saturating substrate concentrations. Transcarbamoylase activity was strongly inhibited by UTP, ADP, ATP, GTP and pyrophosphate.

Aspartate transcarbamylase from the hyperthermophilic archaeon Pyrococcus abyssi. Insights into cooperative and allosteric mechanisms

Aspartate transcarbamylase (ATCase) (EC 2.1.3.2) from the hyperthermophilic archaeon Pyrococcus abyssi was purified from recombinant Escherichia coli cells. The enzyme has the molecular organization of class B microbial aspartate transcarbamylases whose prototype is the E. coli enzyme. P. abyssi ATCase is cooperative towards aspartate. Despite constraints imposed by adaptation to high temperature, the transition between T- and R-states involves significant changes in the quaternary structure, which were detected by analytical ultracentrifugation. The enzyme is allosterically regulated by ATP (activator) and by CTP and UTP (inhibitors). Nucleotide competition experiments showed that these effectors compete for the same sites. At least two regulatory properties distinguish P. abyssi ATCase from E. coli ATCase: (a) UTP by itself is an inhibitor; (b) whereas ATP and UTP act at millimolar concentrations, CTP inhibits at micromolar concentrations, suggesting that in P. abyssi, inhibition by CTP is the major control of enzyme activity. While V(max) increased with temperature, cooperative and allosteric effects were little or not affected, showing that molecular adaptation to high temperature allows the flexibility required to form the appropriate networks of interactions. In contrast to the same enzyme in P. abyssi cellular extracts, the pure enzyme is inhibited by the carbamyl phosphate analogue phosphonacetate; this difference supports the idea that in native cells ATCase interacts with carbamyl phosphate synthetase to channel the highly thermolabile carbamyl phosphate.

Regulation of pyrimidine synthesis in Pseudomonas resinovorans

AIMS

To investigate the regulation of de novo pyrimidine biosynthesis in the bacterium Pseudomonas resinovorans ATCC 14235.

METHODS AND RESULTS

The pyrimidine biosynthetic pathway enzymes were measured in cell extracts from P. resinovorans ATCC 14235 and from an auxotroph lacking orotate phosphoribosyltransferase activity. Pyrimidine biosynthetic pathway enzyme activities in ATCC 14235 were affected by the addition of pyrimidine bases to the culture medium. The de novo enzyme activities of the phosphoribosyltransferase mutant strain increased after pyrimidine starvation indicating possible repression of the pathway by a pyrimidine-related compound. Aspartate transcarbamoylase activity in ATCC 14235 was inhibited in vitro by ATP, UTP and pyrophosphate.

CONCLUSIONS

Pyrimidine biosynthesis in P. resinovorans was regulated at the level of enzyme synthesis and at the level of activity for aspartate transcarbamoylase. Its regulation of enzyme synthesis seemed to be similar to what has been observed in the taxonomically related species Pseudomonas oleovorans.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study found that pyrimidine biosynthesis is regulated in P. resinovorans. This could prove helpful to future studies investigating polyhydroxyalkanoate production by the bacterium.

Pravastatin Restores DDAH Activity and Endothelium-Dependent Relaxation of Rat Aorta After Exposure to Glycated Protein

This study was designed to investigate whether glycated bovine serum albumin (AGE-BSA) inhibits dimethylarginine dimethylaminohydrolase (DDAH) activity to contribute to its adverse effect on endothelium-dependent relaxation in rat aorta, and whether pravastatin reverses the inhibition of DDAH activity and endothelial dysfunction induced by AGE-BSA. Endothelium-dependent relaxation of aortic rings was measured by isometric tension recording, and DDAH activity, and the contents of nitrite/nitrate as well as malondialdehyde (MDA) in aortic tissue were determined after exposure of Sprague-Dawley rat aorta to AGE-BSA (1.70 mmol/L) for 60 minutes in the presence or absence of pravastatin. In comparison with control, both endothelium-dependent relaxation and DDAH activity (0.032 +/- 0.002 versus 0.095 +/- 0.003 U/g protein, n = 5, P < 0.01) were significantly inhibited in isolated rat aorta after exposure to AGE-BSA, which was accompanied by decreases of nitrite/nitrate contents and elevations of MDA levels in aorta. Treatment with pravastatin (1 mmol/L) not only prevented the inhibition of endothelial function but also reversed the decrease of DDAH activity induced by AGE-BSA and normalized the alterations in nitrite/nitrate and MDA contents. Similar effects were observed when rat aorta exposed to AGE-BSA in the presence of antioxidant pyrrolidine dithiocharbamate (PDTC, 30 micromol/L) or protein kinase C inhibitor chelerythrine (1 micromol/L). These results suggested that decreased DDAH activity may be involved in endothelial dysfunction of rat aorta induced by AGE-BSA, and that pravastatin restores DDAH activity and endothelium-dependent relaxation after aorta exposure to AGE-BSA, which may be secondary to its antioxidative effects.

Analysis of Pyrimidine Synthesis “de Novo” Intermediates in Urine and Dried Urine Filter- Paper Strips with HPLC–Electrospray Tandem Mass Spectrometry

Background: The concentrations of the pyrimidine “de novo” metabolites and their degradation products in urine are useful indicators for the diagnosis of an inborn error of the pyrimidine de novo pathway or a urea-cycle defect. Until now, no procedure was available that allowed the analysis of all of these metabolites in a single analytical run. We describe a rapid, specific method to measure these metabolites by HPLC–tandem mass spectrometry.

Methods: Urine or urine-soaked filter-paper strips were used to measure N-carbamyl-aspartate, dihydroorotate, orotate, orotidine, uridine, and uracil. Reversed-phase HPLC was combined with electrospray ionization tandem mass spectrometry, and detection was performed by multiple-reaction monitoring. Stable-isotope-labeled reference compounds were used as internal standards.

Results: All pyrimidine de novo metabolites and their degradation products were measured within a single analytical run of 14 min with lower limits of detection of 0.4–3 μmol/L. The intra- and interassay variation for urine with added compounds was 1.2–5% for urines and 2–9% for filter-paper extracts of the urines. Recoveries of the added metabolites were 97–106% for urine samples and 97–115% for filter-paper extracts of the urines. Analysis of urine samples from patients with a urea-cycle defect or pyrimidine degradation defect showed an aberrant metabolic profile when compared with controls.

Conclusion: HPLC with electrospray ionization tandem mass spectrometry allows rapid testing for disorders affecting the pyrimidine de novo pathway. The use of filter-paper strips could facilitate collection, transport, and storage of urine samples.

Pyrimidine nucleotide synthesis in Pseudomonas citronellolis

Pyrimidine biosynthesis was active in Pseudomonas citronellolis ATCC 13674 and appeared to be regulated by pyrimidines. When wild-type cells were grown on succinate in the presence of uracil, the de novo enzyme activities were depressed while only four enzyme activities were depressed in the glucose-grown cells. On either carbon source, orotic acid-grown cells had diminished aspartate transcarbamoylase, dihydroorotase or OMP decarboxylase activity. Pyrimidine limitation of glucose-grown pyrimidine auxotrophic cells resulted in de novo enzyme activities, except for transcarbamoyolase activity, that were elevated by more than 5-fold compared to their activities in uracil-grown cells. Since pyrimidine limitation of succinate-grown mutant cells produced less enzyme derepression, catabolite repression appeared to be a factor. At the level of enzyme activity, aspartate transcarbamoylase activity in P. citronellolis was strongly inhibited by all effectors tested. Compared to the regulation of pyrimidine biosynthesis in taxonomically-related species, pyrimidine biosynthesis in P. citronellolis appeared more highly regulated.

Aquifex aeolicus dihydroorotase: association with aspartate transcarbamoylase switches on catalytic activity

Dihydroorotase (DHOase) catalyzes the reversible condensation of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. The enzyme from Aquifex aeolicus, a hyperthermophilic organism of ancient lineage, was cloned and expressed in Escherichia coli. The purified protein was found to be a 45-kDa monomer containing a single zinc ion. Although there is no other DHOase gene in the A. aeolicus genome, the recombinant protein completely lacked catalytic activity at any temperature tested. However, DHOase formed an active complex with aspartate transcarbamoylase (ATCase) from the same organism. Whereas the k(cat) of 13.8 +/- 0.03 s(-1) was close to the value observed for the mammalian enzyme, the K (m)for dihydroorotate, 3.03 +/- 0.05 mM was 433-fold higher. Gel filtration and chemical cross-linking showed that the complex exists as a 240-kDa hexamer (DHO(3)-ATC(3)) and a 480-kDa duodecamer (DHO(6)-ATC(6)) probably in rapid equilibrium. Complex formation protects both DHOase and ATCase against thermal degradation at temperatures near 100 degrees C where the organism grows optimally. These results lead to the reclassification of both enzymes: ATCase, previously considered a Class C homotrimer, now falls into Class A, whereas the DHOase is a Class 1B enzyme. CD spectroscopy indicated that association with ATCase does not involve a significant perturbation of the DHOase secondary structure, but the visible absorption spectrum of a Co(2+)-substituted DHOase is appreciably altered upon complex formation suggesting a change in the electronic environment of the active site. The association of DHOase with ATCase probably serves as a molecular switch that ensures that free, uncomplexed DHOase in the cell remains inactive. At pH 7.4, the equilibrium ratio of carbamoyl aspartate to dihydroorotate is 17 and complex formation may drive the reaction in the biosynthetic direction.

Arginine Deiminase Uses an Active-Site Cysteine in Nucleophilic Catalysis ofl-Arginine Hydrolysis

Arginine deiminase (EC 3.5.3.6) catalyzes the hydrolysis of l-arginine to citrulline and ammonium ion, which is the first step of the microbial l-arginine degradation pathway. The deiminase conserves the active-site Cys-His-Asp motif found in several related enzymes that catalyze group-transfer reactions from the guanidinium center of arginine-containing substrates. For each of these enzymes, nucleophilic catalysis by the conserved Cys has been postulated but never tested. In this communication we report the results from rapid quench studies of single-turnover reactions carried out with recombinant Pseudomonas aeruginosa arginine deiminase and limiting [14C-1]l-arginine. The citrulline-formation and arginine-decay curves measured at 25 degrees C were fitted to yield apparent rate constants k = 3.6 +/- 0.1 s-1 and k = 4.2 +/- 0.1 s-1, respectively. The time course for the formation (k =13 s-1) and decay (k = 6.5 s-1) of 14C-labeled enzyme defined a kinetically competent intermediate. Under the same reaction conditions, the Cys406Ser mutant failed to form the 14C-labeled enzyme intermediate. These results, along with the recently reported enzyme X-ray structure (Galkin, A.; Kulakova, L.; Sarikaya, E.; Lim, K.; Howard, A.; Herzberg, O. J. Biol. Chem. 2004, 279, 14001-14008, evidence a reaction pathway in which l-arginine deimination proceeds via a covalent enzyme intermediate formed by ammonia displacement from the arginine guanidinum carbon by the active-site Cys406.

Regulation of pyrimidine nucleotide formation in Pseudomonas reptilivora

AIMS

To study the regulation of de novo pyrimidine biosynthesis in the pathogenic bacterium Pseudomonas reptilivora ATCC 14836.

METHODS AND RESULTS

The pyrimidine biosynthetic pathway enzymes were assayed in extracts of Ps. reptilivora ATCC 14836 cells and of cells from an auxotroph lacking aspartate transcarbamoylase activity. Pyrimidine biosynthetic pathway enzyme activities in ATCC 14836 were influenced by the addition of pyrimidine bases to the culture medium with orotic acid addition inducing dihydroorotase activity. Pyrimidine starvation of the transcarbamoylase mutant strain increased its de novo enzyme activities suggesting that the de novo pathway was also subject to repression by a pyrimidine-related compound. Aspartate transcarbamoylase activity in ATCC 14836 was inhibited in vitro by pyrophosphate and ATP.

CONCLUSIONS

Regulation of pyrimidine biosynthesis in Ps. reptilivora was observed at the level of enzyme synthesis and at the level of activity for aspartate transcarbamoylase. Its regulation of enzyme synthesis seemed to be more highly controlled than what was observed in the related species Ps. fluorescens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This investigation found that pyrimidine biosynthesis is controlled in Ps. reptilivora. This could prove helpful to future studies exploring its pathogenicity.

Effect of shear stress on asymmetric dimethylarginine release from vascular endothelial cells

We demonstrated recently that plasma concentrations of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide (NO) synthase, are increased by high salt intake concomitantly with a decrease in plasma levels of NO in human hypertension. We investigated the effect of shear stress on ADMA release in 2 types of cells: transformed human umbilical vein endothelial cells (HUVECs; cell line ECV-304) and HUVECs. Exposure of ECV-304 cells and HUVECs to shear stress with the use of a cone-plate viscometer enhanced gene expression of protein arginine methyltransferase (PRMT-1), ADMA synthase. In HUVECs, the ratio of PRMT-1 to glyceraldehyde 3-phosphate dehydrogenase mRNA was increased by 2-fold by a shear stress of > or =15 dyne/cm2. A dominant-negative mutant of IkappaB kinase alpha and troglitazone at 8 micromol/L, an activator of peroxisome proliferator-activated receptor gamma, abolished the shear stress-induced increase in PRMT-1 gene expression in parallel with the blockade of nuclear factor (NF)-kappaB translocation into the nucleus. The activity of dimethylarginine dimethylaminohydrolase, the degradation enzyme of ADMA, was unchanged after shear stress < or =15 dyne/cm2 and was enhanced by 1.48+/-0.06-fold (P<0.05) by shear stress at 25 dyne/cm2. The release of ADMA was increased by 1.64+/-0.10-fold (P<0.05) by shear stress at 15 dyne/cm2 but was not affected by shear stress at 25 dyne/cm2. These results indicate that shear stress enhances gene expression of PRMT-1 and ADMA release via activation of the NF-kappaB pathway. Shear stress at higher magnitudes facilitates the degradation of ADMA, thus returning ADMA release levels to baseline.

Aquifex aeolicus aspartate transcarbamoylase, an enzyme specialized for the efficient utilization of unstable carbamoyl phosphate at elevated temperature

Aquifex aeolicus, an organism that flourishes at 95 degrees C, is one of the most thermophilic eubacteria thus far described. The A. aeolicus pyrB gene encoding aspartate transcarbamoylase (ATCase) was cloned, overexpressed in Escherichia coli, and purified by affinity chromatography to a homogeneous form that could be crystallized. Chemical cross-linking and size exclusion chromatography showed that the protein was a homotrimer of 34-kDa catalytic chains. The activity of A. aeolicus ATCase increased dramatically with increasing temperature due to an increase in kcat with little change in the Km for the substrates, carbamoyl phosphate and aspartate. The Km for both substrates was 30-40-fold lower than the corresponding values for the homologous E. coli ATCase catalytic subunit. Although rapidly degraded at high temperature, the carbamoyl phosphate generated in situ by A. aeolicus carbamoyl phosphate synthetase (CPSase) was channeled to ATCase. The transient time for carbamoyl aspartate formation was 26 s, compared with the much longer transient times observed when A. aeolicus CPSase was coupled to E. coli ATCase. Several other approaches provided strong evidence for channeling and transient complex formation between A. aeolicus ATCase and CPSase. The high affinity for substrates combined with channeling ensures the efficient transfer of carbamoyl phosphate from the active site of CPSase to that of ATCase, thus preserving it from degradation and preventing the formation of toxic cyanate.

Yeast epiarginase regulation, an enzyme-enzyme activity control: identification of residues of ornithine carbamoyltransferase and arginase responsible for enzyme catalytic and regulatory activities

In the presence of ornithine and arginine, ornithine carbamoyltransferase (OTCase) and arginase form a one-to-one enzyme complex in which the activity of OTCase is inhibited whereas arginase remains catalytically active. The mechanism by which these nonallosteric enzymes form a stable complex triggered by the binding of their respective substrates raises the question of how such a cooperative association is induced. Analyses of mutations in both enzymes identify residues that are required for their association, some of them being important for catalysis. In arginase, two cysteines at the C terminus of the protein are crucial for its epiarginase function but not for its catalytic activity and trimeric structure. In OTCase, mutations of putative ornithine binding residues, Asp-182, Asn-184, Asn-185, Cys-289, and Glu-256 greatly reduced the affinity for ornithine and impaired the interaction with arginase. The four lysine residues located in the SMG loop, Lys-260, Lys-263, Lys-265, and Lys-268, also play an important role in mediating the sensitivity of OTCase to ornithine and to arginase and appear to be involved in transducing and enhancing the signal given by ornithine for the closure of the catalytic domain.

Aspartate transcarbamylase from the hyperthermophilic archaeon Pyrococcus abyssi: thermostability and 1.8A resolution crystal structure of the catalytic subunit complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate

The Pyrococcus abyssi aspartate transcarbamylase (ATCase) shows a high degree of structural conservation with respect to the well-studied mesophilic Escherichia coli ATCase, including the association of catalytic and regulatory subunits. The adaptation of its catalytic function to high temperature was investigated, using enzyme purified from recombinant E.coli cells. At 90 degrees C, the activity of the trimeric catalytic subunit was shown to be intrinsically thermostable. Significant extrinsic stabilization by phosphate, a product of the reaction, was observed when the temperature was raised to 98 degrees C. Comparison with the holoenzyme showed that association with regulatory subunits further increases thermostability. To provide further insight into the mechanisms of its adaptation to high temperature, the crystal structure of the catalytic subunit liganded with the analogue N-phosphonacetyl-L-aspartate (PALA) was solved to 1.8A resolution and compared to that of the PALA-liganded catalytic subunit from E.coli. Interactions with PALA are strictly conserved. This, together with the similar activation energies calculated for the two proteins, suggests that the reaction mechanism of the P.abyssi catalytic subunit is similar to that of the E.coli subunit. Several structural elements potentially contributing to thermostability were identified: (i) a marked decrease in the number of thermolabile residues; (ii) an increased number of charged residues and a concomitant increase of salt links at the interface between the monomers, as well as the formation of an ion-pair network at the protein surface; (iii) the shortening of three loops and the shortening of the N and C termini. Other known thermostabilizing devices such as increased packing density or reduction of cavity volumes do not appear to contribute to the high thermostability of the P.abyssi enzyme.

Control of pyrimidine synthesis in Pseudomonas fragi

AIMS

To study the regulation of the de novo pyrimidine biosynthetic enzymes in the food-spoilage agent Pseudomonas fragi ATCC 4973.

METHODS AND RESULTS

The de novo pyrimidine biosynthetic enzymes were measured in extracts of Ps. fragi ATCC 4973 cells and of cells from auxotrophs deficient for dihydroorotase or OMP decarboxylase activity. Pyrimidine biosynthetic enzyme activities in ATCC 4973 were influenced by pyrimidine supplementation to the culture medium. The pyrimidine limitation of each auxotroph elevated the de novo enzyme activities, indicating that this pathway may be repressible by a pyrimidine-related compound. Aspartate transcarbamoylase activity in ATCC 4973 was inhibited in vitro by pyrophosphate and purine or pyrimidine nucleotides.

CONCLUSIONS

Pyrimidine synthesis in Ps. fragi appeared to be controlled at the transcriptional level and at the level of activity for aspartate transcarbamoylase. Its transcriptional regulation seemed to be more highly controlled than what was observed in the closely related species Pseudomonas putida and Pseudomonas fluorescens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that pyrimidine synthesis is regulated in Ps. fragi. This could prove useful to future studies examining its biological control and its taxonomic assignment.

Control of pyrimidine formation in Pseudomonas putida ATCC 17536

The regulation of de novo pyrimidine biosynthesis in Pseudomonas putida ATCC 17536 by pyrimidines was explored. The pathway enzyme activities were higher in glucose-grown cells than in succinate-grown cells, indicating catabolite repression by succinate. In P. putida cells grown on succinate as a carbon source, only aspartate transcarbamoylase activity was greatly diminished by uracil supplementation. When glucose was the carbon source, orotic acid supplementation significantly decreased orotate phosphoribosyltransferase and orotidine 5'-monophosphate (OMP) decarboxylase activities. Uracil auxotrophs, deficient for dihydroorotase activity or with reduced phosphoribosyltransferase activity, were isolated. After pyrimidine limitation of both auxotrophs, the greatest derepression of enzyme activity was observed for OMP decarboxylase independent of carbon source. Orotic acid induced both phosphoribosyltransferase and decarboxylase activities in glucose-grown cells of the dihydroorotase-deficient strain. Regulation at the transcriptional level of de novo pyrimidine biosynthetic enzyme synthesis in P. putida ATCC 17536 was observed, which contrasts with previous observations.

Unmasking a functional allosteric domain in an allosterically nonresponsive carbamoyl-phosphate synthetase

Although carbamoyl-phosphate synthetases (CPSs) share sequence identity, multidomain structure, and reaction mechanism, they have varying physiological roles and allosteric effectors. Escherichia coli CPS (eCPS) provides CP for both arginine and pyrimidine nucleotide biosynthesis and is allosterically regulated by metabolites from both pathways, with inhibition by UMP and activation by IMP and ornithine. The arginine-specific CPS from Saccharomyces cerevisiae (sCPS), however, apparently responds to no allosteric effectors. We have designed and analyzed a chimeric CPS (chCPS, in which the C-terminal 136 residues of eCPS were replaced by the corresponding residues of sCPS) to define the structural basis for the allosteric nonresponsiveness of sCPS and thereby provide insight into the mechanism for allosteric selectivity and responsiveness in the other CPSs. Surprisingly, ornithine and UMP each had a significant effect on chCPS activity, and did so at concentrations that were similar to those effective for eCPS. We further found that sCPS bound both UMP and IMP and that chCPS bound IMP, although none of these interactions led to changes in enzymatic activity. These findings strongly suggest that the nonresponsive sCPS is not able to communicate occupancy of the allosteric site to the active site but does contain a latent allosteric interaction domain.

Autophosphorylation of the mammalian multifunctional protein that initiates de novo pyrimidine biosynthesis

CAD, a large multifunctional protein that carries carbamoyl phosphate synthetase (CPSase), aspartate transcarbamoylase, and dihydroorotase activities, catalyzes the first three steps of de novo pyrimidine biosynthesis in mammalian cells. The CPSase component, which catalyzes the initial, rate-limiting step, exhibits complex regulatory mechanisms involving allosteric effectors and phosphorylation that control the flux of metabolites through the pathway. Incubation of CAD with ATP in the absence of exogenous kinases resulted in the incorporation of 1 mol of P(i)/mol of CAD monomer. Mass spectrometry analysis of tryptic digests showed that Thr(1037) located within the CAD CPS.B subdomain was specifically modified. The reaction is specific for MgATP, ADP was a competitive inhibitor, and the native tertiary structure of the protein was required. Phosphorylation occurred after denaturation, further purification of CAD by SDS gel electrophoresis, and renaturation on a nitrocellulose membrane, strongly suggesting that phosphate incorporation resulted from an intrinsic kinase activity and was not the result of contaminating kinases. Chemical modification with the ATP analog, 5'-p-fluorosulfonylbenzoyladenosine, showed that one or both of the active sites that catalyze the ATP-dependent partial reactions are also involved in autophosphorylation. The rate of phosphorylation was dependent on the concentration of CAD, indicating that the reaction was, at least in part, intermolecular. Autophosphorylation resulted in a 2-fold increase in CPSase activity, an increased sensitivity to the feedback inhibitor UTP, and decreased allosteric activation by 5-phosphoribosyl-1-pyrophosphate, functional changes that were distinctly different from those resulting from phosphorylation by either the protein kinase A or mitogen-activated protein kinase cascades.

Pseudomonas aeruginosa aspartate transcarbamoylase. Characterization of its catalytic and regulatory properties

Aspartate transcarbamoylase from Pseudomonadaceae is a class A enzyme consisting of six copies of a 36-kDa catalytic chain and six copies of a 45-kDa polypeptide of unknown function. The 45-kDa polypeptide is homologous to dihydroorotase but lacks catalytic activity. Pseudomonas aeruginosa aspartate transcarbamoylase was overexpressed in Escherichia coli. The homogeneous His-tagged protein isolated in high yield, 30 mg/liter of culture, by affinity chromatography and crystallized. Attempts to dissociate the catalytic and pseudo-dihydroorotase (pDHO) subunits or to express catalytic subunits only were unsuccessful suggesting that the pDHO subunits are required for the proper folding and assembly of the complex. As reported previously, the enzyme was inhibited by micromolar concentrations of all nucleotide triphosphates. In the absence of effectors, the aspartate saturation curves were hyperbolic but became strongly sigmoidal in the presence of low concentrations of nucleotide triphosphates. The inhibition was unusual in that only free ATP, not MgATP, inhibits the enzyme. Moreover, kinetic and binding studies with a fluorescent ATP analog suggested that ATP induces a conformational change that interferes with the binding of carbamoyl phosphate but has little effect once carbamoyl phosphate is bound. The peculiar allosteric properties suggest that the enzyme may be a potential target for novel chemotherapeutic agents designed to combat Pseudomonas infection.

Pyrimidine biosynthesis in Pseudomonas oleovorans

AIMS

To investigate the regulation of de novo pyrimidine biosynthesis in the polyhydroxyalkanoate-producing bacterium Pseudomonas oleovorans at the level of enzyme synthesis and at the level of aspartate transcarbamoylase activity.

METHODS AND RESULTS

The effect of pyrimidine supplementation on the pyrimidine biosynthetic pathway enzyme activities was analysed relative to carbon source. Two uracil auxotrophs of P. oleovorans were isolated that were deficient for aspartate transcarbamoylase or dihydroorotase activity. Pyrimidine limitation of these auxotrophs increased the de novo pathway activities to varying degrees depending on the pathway mutation and the carbon source utilized. At the level of aspartate transcarbamoylase activity, pyrophosphate and uridine ribonucleotides were found to be strongly inhibitory of the Ps. oleovorans enzyme.

CONCLUSIONS

Pyrimidine biosynthesis is regulated in Ps. oleovorans. Taxonomically, the regulation of the pyrimidine biosynthetic pathway appeared dissimilar from previously studied Pseudomonas species.

SIGNIFICANCE AND IMPACT OF THE STUDY

New insights regarding the regulation of nucleic acid metabolism are provided that could prove significant during the genetic manipulation of Ps. oleovorans to increase the synthesis of polyhydroxyalkanoates.

Metabolic channeling of carbamoyl phosphate, a thermolabile intermediate: evidence for physical interaction between carbamate kinase-like carbamoyl-phosphate synthetase and ornithine carbamoyltransferase from the hyperthermophile Pyrococcus furiosus

Two different approaches provided evidence for a physical interaction between the carbamate kinase-like carbamoyl-phosphate synthetase (CKase) and ornithine carbamoyltransferase (OTCase) from the hyperthermophilic archaeon Pyrococcus furiosus. Affinity electrophoresis indicated that CKase and OTCase associate into a multienzyme cluster. Further evidence for a biologically significant interaction between CKase and OTCase was obtained by co-immunoprecipitation combined with formaldehyde cross-linking experiments. These experiments support the hypothesis that CKase and OTCase form an efficient channeling cluster for carbamoyl phosphate, an extremely thermolabile and potentially toxic metabolic intermediate. Therefore, by physically interacting with each other, CKase and OTCase prevent the thermodenaturation of carbamoyl phosphate in the aqueous cytoplasmic environment.

Growth-dependent regulation of mammalian pyrimidine biosynthesis by the protein kinase A and MAPK signaling cascades

The carbamoyl phosphate synthetase domain of the multifunctional protein CAD catalyzes the initial, rate-limiting step in mammalian de novo pyrimidine biosynthesis. In addition to allosteric regulation by the inhibitor UTP and the activator PRPP, the carbamoyl phosphate synthetase activity is controlled by mitogen-activated protein kinase (MAPK)- and protein kinase A (PKA)-mediated phosphorylation. MAPK phosphorylation, both in vivo and in vitro, increases sensitivity to PRPP and decreases sensitivity to the inhibitor UTP, whereas PKA phosphorylation reduces the response to both allosteric effectors. To elucidate the factors responsible for growth state-dependent regulation of pyrimidine biosynthesis, the activity of the de novo pyrimidine pathway, the MAPK and PKA activities, the phosphorylation state, and the allosteric regulation of CAD were measured as a function of growth state. As cells entered the exponential growth phase, there was an 8-fold increase in pyrimidine biosynthesis that was accompanied by a 40-fold increase in MAPK activity and a 4-fold increase in CAD threonine phosphorylation. PRPP activation increased to 21-fold, and UTP became a modest activator. These changes were reversed when the cultures approach confluence and growth ceases. Moreover, CAD phosphoserine, a measure of PKA phosphorylation, increased 2-fold in confluent cells. These results are consistent with the activation of CAD by MAPK during periods of rapid growth and its down-regulation in confluent cells associated with decreased MAPK phosphorylation and a concomitant increase in PKA phosphorylation. A scheme is proposed that could account for growth-dependent regulation of pyrimidine biosynthesis based on the sequential action of MAPK and PKA on the carbamoyl phosphate synthetase activity of CAD.

Replacement of Asp-162 by Ala prevents the cooperative transition by the substrates while enhancing the effect of the allosteric activator ATP on E. coli aspartate transcarbamoylase

The available crystal structures of Escherichia coli aspartate transcarbamoylase (ATCase) show that the conserved residue Asp-162 from the catalytic chain interacts with essentially the same residues in both the T- and R-states. To study the role of Asp-162 in the regulatory properties of the enzyme, this residue has been replaced by alanine. The mutant D162A shows a 7700-fold reduction in the maximal observed specific activity, a twofold decrease in the affinity for aspartate, a loss of homotropic cooperativity, and decreased activation by the nucleotide effector adenosine triphosphate (ATP) compared with the wild-type enzyme. Small-angle X-ray scattering (SAXS) measurements reveal that the unliganded mutant enzyme adopts the T-quaternary structure of the wild-type enzyme. Most strikingly, the bisubstrate analog N-phosphonacetyl-L-aspartate (PALA) is unable to induce the T to R quaternary structural transition, causing only a small alteration of the scattering pattern. In contrast, addition of the activator ATP in the presence of PALA causes a significant increase in the scattering amplitude, indicating a large quaternary structural change, although the mutant does not entirely convert to the wild-type R structure. Attempts at modeling this new conformation using rigid body movements of the catalytic trimers and regulatory dimers did not yield a satisfactory solution. This indicates that intra- and/or interchain rearrangements resulting from the mutation bring about domain movements not accounted for in the simple model. Therefore, Asp-162 appears to play a crucial role in the cooperative structural transition and the heterotropic regulatory properties of ATCase.

Characterization of the interaction of Bacillus subtilis PyrR with pyr mRNA by site-directed mutagenesis of the protein

The Bacillus subtilis PyrR protein regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine nucleotide-dependent manner to specific sites on pyr mRNA and stabilizing a secondary structure of the downstream RNA that favors termination of transcription. The high-resolution structure of unliganded PyrR was used to guide site-directed mutagenesis of 12 amino acid residues that were thought likely to be involved in the binding of RNA. Missense mutations were constructed and evaluated for their effects on regulation of pyr genes in vivo and their uracil phosphoribosyltransferase activity, which is catalyzed by wild-type PyrR. A substantial fraction of the mutant PyrR proteins did not have native structures, but eight PyrR mutants were purified and characterized physically, for their uracil phosphoribosyltransferase activity and for their ability to bind pyr RNA in vitro. On the basis of these studies Thr-18, His-22, Arg-141, and Arg-146 were implicated in RNA binding. Arg-27 and Lys-152 were also likely to be involved in RNA binding, but Gln substitution mutations in these residues may have altered their subunit-subunit interactions slightly. Arg-19 was implicated in pyr regulation, but a specific role in RNA binding could not be demonstrated because the R19Q mutant protein could not be purified in native form. The results confirm a role in RNA binding of a positively charged face of PyrR previously identified from the crystallographic structure. The RNA binding residues lie in two sequence segments that are conserved in PyrR proteins from many species.

Molecular cloning, recombinant expression and partial characterization of the aspartate transcarbamoylase from Toxoplasma gondii

A cDNA coding for a monofunctional aspartate transcarbamoylase (ATCase) was isolated from a Toxoplasma gondii tachyzoite cDNA library using a complementation method. The calculated molecular mass of the deduced amino acid sequence was 46.8 kDa, with a predicted pI of 7.1. Size exclusion chromatography/laser-light scattering showed a single, monodisperse peak with molecular mass of 144 kDa. Amino acid sequence alignments revealed that active site residues of the Escherichia coli ATCase catalytic chain were conserved in the T. gondii sequence, and the latter shared 26-33% overall sequence identity with other ATCases. A recombinant enzyme was overexpressed in E. coli, and was purified with a yield of approximately 0.8 mg l(-1) culture. The temperature dependence of the recombinant enzyme was similar to that of native ATCase in T. gondii extracts. The K(m)'s for aspartate and carbamoyl phosphate were 7.82 mM, and 67.6 microM, respectively. The V(max) was 23900 micromol h(-1) mg(-1). Pyrimidine nucleotides had no significant effect on the enzyme's activity. N-phosphonoacetyl-L-aspartate (PALA) inhibited the enzyme with K(i)=0.38 microM. The T. gondii ATCases contained two additional sequences of approximately 24 residues each, which are not found in other ATCases. One of these sequences was susceptible to proteolysis by elastase.

An enzyme hydrolyzing methylated inhibitors of nitric oxide synthase is present in circulating human red blood cells

N(G),N(G)-dimethyl-L-arginine (asymmetric dimethylarginine or ADMA) and N(G)-monomethyl-L-arginine (L-NMMA) are post-translationally synthesized amino acids of nuclear proteins. Upon release during protein turnover, they are not used in protein synthesis, but are excreted or metabolized by dimethylarginine dimethylaminohydrolase (DDAH) found in many tissues. DDAH is present in monocytic and polynuclear cells of blood, but no report has appeared of its presence in red blood cells (RBCs). Because methylated arginines can inhibit nitric oxide synthase (NOS) and elevations are reported in several diseases, we explored whether RBCs express this enzyme. DDAH is present in RBCs as supported by hydrolysis of both ADMA and L-NMMA, but not symmetric dimethylarginine, and by immunoprecipitation/Westem blot using a specific monoclonal antibody to human DDAH. In a pilot study of end-stage renal disease (ESRD) patients, RBC DDAH activity with ADMA as substrate correlated inversely with age (p = 0.005) and enzyme activities were higher in patients with greater diastolic blood pressure drops during hemodialysis (p = 0.02). Similar correlations were found with white cell DDAH activity. Thus, human RBCs can hydrolyze methylated arginines. These findings indicate the RBC could be used to assess the status of DDAH in various disease states.

Homocysteine impairs the nitric oxide synthase pathway: role of asymmetric dimethylarginine

BACKGROUND

Hyperhomocysteinemia is a putative risk factor for cardiovascular disease, which also impairs endothelium-dependent vasodilatation. A number of other risk factors for cardiovascular disease may exert their adverse vascular effects in part by elevating plasma levels of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthase. Accordingly, we determined if homocysteine could increase ADMA levels.

METHODS AND RESULTS

When endothelial or nonvascular cells were exposed to DL-homocysteine or to its precursor L-methionine, ADMA concentration in the cell culture medium increased in a dose- and time-dependent fashion. This effect was associated with the reduced activity of dimethylarginine dimethylaminohydrolase (DDAH), the enzyme that degrades ADMA. Furthermore, homocysteine-induced accumulation of ADMA was associated with reduced nitric oxide synthesis by endothelial cells and segments of pig aorta. The antioxidant pyrrollidine dithiocarbamate preserved DDAH activity and reduced ADMA accumulation. Moreover, homocysteine dose-dependently reduced the activity of recombinant human DDAH in a cell free system, an effect that was due to a direct interaction between homocysteine and DDAH.

CONCLUSION

Homocysteine post-translationally inhibits DDAH enzyme activity, causing ADMA to accumulate and inhibit nitric oxide synthesis. This may explain the known effect of homocysteine to impair endothelium-mediated nitric oxide-dependent vasodilatation.

Metabolism of S-nitrosoglutathione in intact mitochondria

S-nitrosation of protein thiol groups by nitric oxide (NO*) is a widely recognized protein modification. Only few intracellular S-nitrosated proteins have been identified and it has been reported that S-nitrosation/denitrosation can serve as a regulatory process in signal-transduction pathways. Given the potential physiological importance of S-nitrosothiols, and considering that mitochondria are endowed with high levels of thiols and the biochemical requisites for synthesizing NO*, we examined the occurrence of S-nitrosoglutathione (GSNO) in intact, coupled rat liver mitochondria. These organelles contained 0.34 nmol of GSNO/mg of protein, detected by HPLC with UV-visible and electrochemical detections. This concentration was dynamically modulated by the availability of NO*; its decay was affected mainly by GSH and superoxide dismutase in a reaction that entailed the generation of GSSG. On the basis of the relatively long half-life of GSNO and the negligible recovery of NO* during its decay, roles for GSNO as a storage and transport molecule for NO* are discussed. Moreover, the formation of GSNO and its reaction with GSH can be considered to be partly responsible for the catabolism of NO* via a complex mechanism that might result in the formation of hydroxylamine, nitrite or nitrous oxide depending upon the availability of oxygen, superoxide dismutase and glutathione. Finally, the high concentrations of GSH in the cytosol and mitochondria might favour the formation of GSNO by reacting with NO* 'in excess', thereby avoiding damaging side reactions (such as peroxynitrite formation), and facilitate the inactivation of NO* by generating other nitrogen-related species without the chemical properties characteristic of NO*.

Probing the role of oligomerization in the high thermal stability of Pyrococcus furiosus ornithine carbamoyltransferase by site-specific mutants

The Pyrococcus furiosus ornithine carbamoyltransferase (OTCase) is extremely heat stable and maintains 50% of its catalytic activity after 60 min at 100 degrees C. The enzyme has an unusual quaternary structure when compared to anabolic OTCases from mesophilic organisms. It is built up of four trimers arranged in a tetrahedral manner, while other anabolic enzymes are single trimers. Residues Trp21, Glu25, Met29 and Trp33 are located in the main interfaces that occur between the catalytic trimers within the dodecamer. They participate in either hydrophobic clusters or ionic interactions. In order to elucidate the role played by the oligomerization in the enzyme stability at very high temperatures, we performed mutagenesis studies of these residues. All the variants show similar catalytic activities and kinetic properties when compared to the wild-type enzyme, allowing the interpretation of the mutations solely on heat stability and quaternary structure. The W21A variant has only a slight decrease in its stability, and is a dodecamer. The variants E25Q, M29A, W33A, W21A/W33A and E25Q/W33A show that altering more drastically the interfaces results in a proportional decrease in heat stability, correlated with a gradual dissociation of dodecamers into trimers. Finally, the E25Q/M29A/W33A variant shows a very large decrease in heat stability and is a trimer. These results suggest that extreme thermal stabilization of this OTCase is achieved in part through oligomerization.

Nitric oxide synthase in porcine heart mitochondria: evidence for low physiological activity

The capacity of isolated porcine heart mitochondria to produce nitric oxide (NO) via mitochondrial NO synthase (NOS) was evaluated. The mitochondrial NOS content and activity (0.2 nmol NO x mg mitochondrial protein(-1) x min(-1)) were approximately 10 times lower than previously reported for the rat liver. No evidence for mitochondrial NOS-generated NO was found in mitochondrial suspensions based on the lack of NO production and the lack of effect of either L-arginine or NOS inhibitors on the rate of respiration. The reason that even the low mitochondrial NOS activity did not result in net NO production and metabolic effects is because the mitochondrial metabolic breakdown of NO (1-4 nmol NO x mg mitochondrial protein(-1) x min(-1)) was greater than the maximum rate of NO production measured in homogenates. These data suggest that NO production at the mitochondria via NOS is not a significant source of NO in the intact heart and does not regulate cardiac oxidative phosphorylation.

The pyrimidine operon pyrRPB-carA from Lactococcus lactis

The four genes pyrR, pyrP, pyrB, and carA were found to constitute an operon in Lactococcus lactis subsp. lactis MG1363. The functions of the different genes were established by mutational analysis. The first gene in the operon is the pyrimidine regulatory gene, pyrR, which is responsible for the regulation of the expression of the pyrimidine biosynthetic genes leading to UMP formation. The second gene encodes a membrane-bound high-affinity uracil permease, required for utilization of exogenous uracil. The last two genes in the operon, pyrB and carA, encode pyrimidine biosynthetic enzymes; aspartate transcarbamoylase (pyrB) is the second enzyme in the pathway, whereas carbamoyl-phosphate synthetase subunit A (carA) is the small subunit of a heterodimeric enzyme, catalyzing the formation of carbamoyl phosphate. The carA gene product is shown to be required for both pyrimidine and arginine biosynthesis. The expression of the pyrimidine biosynthetic genes including the pyrRPB-carA operon is subject to control at the transcriptional level, most probably by an attenuator mechanism in which PyrR acts as the regulatory protein.

The modulation of oxygen radical production by nitric oxide in mitochondria

Biological systems that produce or are exposed to nitric oxide (NO radical) exhibit changes in the rate of oxygen free radical production. Considering that mitochondria are the main intracellular source of oxygen radicals, and based on the recently documented production of NO(radical) by intact mitochondria, we investigated whether NO(radical), produced by the mitochondrial nitric-oxide synthase, could affect the generation of oxygen radicals. Toward this end, changes in H(2)O(2) production by rat liver mitochondria were monitored at different rates of endogenous NO(radical) production. The observed changes in H(2)O(2) production indicated that NO(radical) affected the rate of oxygen radical production by modulating the rate of O(2) consumption at the cytochrome oxidase level. This mechanism was supported by these three experimental proofs: 1) the reciprocal correlation between H(2)O(2) production and respiratory rates under different conditions of NO(radical) production; 2) the pattern of oxidized/reduced carriers in the presence of NO(radical), which pointed to cytochrome oxidase as the crossover point; and 3) the reversibility of these effects, evidenced in the presence of oxymyoglobin, which excluded a significant role for other NO(radical)-derived species such as peroxynitrite. Other sources of H(2)O(2) investigated, such as the aerobic formation of nitrosoglutathione and the GSH-mediated decay of nitrosoglutathione, were found quantitatively negligible compared with the total rate of H(2)O(2) production.

Allosteric signal transmission involves synergy between discrete structural units of the regulatory subunit of aspartate transcarbamoylase

Previous studies have shown that the S5' beta-strand (r93-r97) of the regulatory polypeptides of the aspartate transcarbamoylases (ATCases) from Serratia marcescens and Escherichia coli are responsible for their diverged allosteric regulatory patterns, including conversion of CTP from an inhibitor in E. coli to an activator in S. marcescens. Similarly, mutation of residues located in the interface between the allosteric and the zinc domains resulted in conversion of the ATP responses of the E. coli enzyme from activation to inhibition, suggesting that this interface not only mediates but also discriminates the allosteric responses of ATP and CTP. To further decipher the roles and the interrelationships of these regions in allosteric communication, allosteric-zinc interface mutations (Y77F and V106A) have been introduced into both the native and the S5' beta-strand chimeric backgrounds. While the significance of this interface in the allosteric regulation has been confirmed, there is no direct evidence supporting the presence of distinct pathways for the ATP and CTP signals through this interface. The analysis of the mutational effects reported here suggested that the S5' beta-strand transmits the allosteric signal by modulating the hydrophobic allosteric-zinc interface rather than disturbing the allosteric ligand binding. Intragenic suppression by substitutions in the hydrophobic interface between the allosteric and the zinc domains of the regulatory chains resulted in the partial recovery of allosteric responses in the EC:rS5'sm chimera and reduced the activation by ATP in the Sm:rS5'ec chimera. Thus, it seems that there is a synergy between these two structural units.

Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase

The native Escherichia coli aspartate transcarbamoylase (ATCase, E.C. 2.1.3.2) provides a classic allosteric model for the feedback inhibition of a biosynthetic pathway by its end products. Both E. coli and Erwinia herbicola possess ATCase holoenzymes which are dodecameric (2(c3):3(r2)) with 311 amino acid residues per catalytic monomer and 153 and 154 amino acid residues per regulatory (r) monomer, respectively. While the quaternary structures of the two enzymes are identical, the primary amino acid sequences have diverged by 14 % in the catalytic polypeptide and 20 % in the regulatory polypeptide. The amino acids proposed to be directly involved in the active site and nucleotide binding site are strictly conserved between the two enzymes; nonetheless, the two enzymes differ in their catalytic and regulatory characteristics. The E. coli enzyme has sigmoidal substrate binding with activation by ATP, and inhibition by CTP, while the E. herbicola enzyme has apparent first order kinetics at low substrate concentrations in the absence of allosteric ligands, no ATP activation and only slight CTP inhibition. In an apparently important and highly conserved characteristic, CTP and UTP impose strong synergistic inhibition on both enzymes. The co-operative binding of aspartate in the E. coli enzyme is correlated with a T-to-R conformational transition which appears to be greatly reduced in the E. herbicola enzyme, although the addition of inhibitory heterotropic ligands (CTP or CTP+UTP) re-establishes co-operative saturation kinetics. Hybrid holoenzymes assembled in vivo with catalytic subunits from E. herbicola and regulatory subunits from E. coli mimick the allosteric response of the native E. coli holoenzyme and exhibit ATP activation. The reverse hybrid, regulatory subunits from E. herbicola and catalytic subunits from E. coli, exhibited no response to ATP. The conserved structure and diverged functional characteristics of the E. herbicola enzyme provides an opportunity for a new evaluation of the common paradigm involving allosteric control of ATCase.

Intramolecular signal transmission in enterobacterial aspartate transcarbamylases II. Engineering co-operativity and allosteric regulation in the aspartate transcarbamylase of Erwinia herbicola

The aspartate transcarbamylase (ATCase) from Erwinia herbicola differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains ((c3)2(r2)3), as other enterobacterial ATCases and shows extensive primary structure conservation. In (c3)2(r2)3 ATCases, the association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. Alignment of the primary sequence of the regulatory polypeptides from the E. herbicola and from the paradigmatic Escherichia coli ATCases reveals major blocks of divergence, corresponding to discrete structural elements in the E. coli enzyme. Chimeric ATCases were constructed by exchanging these blocks of divergent sequence between these two ATCases. It was found that the amino acid composition of the outermost beta-strand of a five-stranded beta-sheet in the effector-binding domain of the regulatory polypeptide is responsible for the lack of co-operativity and response to ATP of the E. herbicola ATCase. A novel structural element involved in allosteric signal recognition and transmission in this family of ATCases was thus identified.

Aspartate carbamoyltransferase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. Cloning, sequence analysis, enzyme purification and characterization

The genes coding for aspartate carbamoyltransferase (ATCase) in the extremely thermophilic archaeon Sulfolobus acidocaldarius have been cloned by complementation of a pyrBI deletion mutant of Escherichia coli. Sequencing revealed the existence of an enterobacterial-like pyrBI operon encoding a catalytic chain of 299 amino acids (34 kDa) and a regulatory chain of 170 amino acids (17.9 kDa). The deduced amino acid sequences of the pyrB and pyrI genes showed 27.6-50% identity with archaeal and enterobacterial ATCases. The recombinant S. acidocaldarius ATCase was purified to homogeneity, allowing the first detailed studies of an ATCase isolated from a thermophilic organism. The recombinant enzyme displayed the same properties as the ATCase synthesized in the native host. It is highly thermostable and exhibits Michaelian saturation kinetics for carbamoylphosphate (CP) and positive homotropic cooperative interactions for the binding of L-aspartate. Moreover, it is activated by nucleoside triphosphates whereas the catalytic subunits alone are inhibited. The holoenzyme purified from recombinant E. coli cells or present in crude extract of the native host have an Mr of 340 000 as estimated by gel filtration, suggesting that it has a quaternary structure similar to that of E. coli ATCase. Only monomers could be found in extracts of recombinant E. coli or Saccharomyces cerevisiae cells expressing the pyrB gene alone. In the presence of CP these monomers assembled into trimers. The stability of S. acidocaldarius ATCase and the allosteric properties of the enzyme are discussed in function of a modeling study.

Serine 948 and threonine 1042 are crucial residues for allosteric regulation of Escherichia coli carbamoylphosphate synthetase and illustrate coupling effects of activation and inhibition pathways

Escherichia coli carbamoylphosphate synthetase (CPSase) is a key enzyme in the pyrimidine nucleotides and arginine biosynthetic pathways. The enzyme harbors a complex regulation, being activated by ornithine and inosine 5'-monophosphate (IMP), and inhibited by UMP. CPSase mutants obtained by in vivo mutagenesis and selected on the basis of particular phenotypes have been characterized kinetically. Two residues, serine 948 and threonine 1042, appear crucial for allosteric regulation of CPSase. When threonine 1042 is replaced by an isoleucine residue, the enzyme displays a greatly reduced activation by ornithine. The T1042I mutated enzyme is still sensitive to UMP and IMP, although the effects of both regulators are reduced. When serine 948 is replaced by phenylalanine, the enzyme becomes insensitive to UMP and IMP, but is still activated by ornithine, although to a reduced extent. When correlating these observations to the structural data recently reported, it becomes clear that both mutations, which are located in spatially distinct regions corresponding respectively to the ornithine and the UMP/IMP binding sites, have coupled effects on the enzyme regulation. These results provide an illustration that coupling of regulatory pathways occurs within the allosteric subunit of E. coli CPSase. In addition, other mutants have been characterized, which display altered affinities for the different CPSase substrates and also slightly modified properties towards the allosteric effectors: P165S, P170L, A182V, P360L, S743N, T800F and G824D. Kinetic properties of these modified enzymes are also presented here and correlated to the crystal structure of E. coli CPSase and to the phenotype of the mutants.

Lack of evidence for antisense suppression in the fungal plant pathogen Ustilago maydis

Modulation of the expression of the Ustilago maydis Pyr3 gene, encoding dihydroorotase (DHOase), through antisense RNA regulation has been explored. This was done by placing the gene in sense and antisense orientations under the control of an hsp70-like gene promoter in a high-copy number autonomously replicating expression vector. Cells transformed with the antisense vector contained similar levels of DHOase activity to those found in cells harboring the expression vector alone. Transformants containing the antisense vector did not exhibit uridine-dependent growth, which would be expected for a Pyr3-deficient phenocopy. This was despite detection of high levels of antisense RNA transcripts in cells transformed with the Pyr3 antisense vector.

Rapid detection of ornithine transcarbamylase activity by micellar electrokinetic chromatography

A quantitative ultraviolet detection method for determining ornithine transcarbamylase (OTC-ase) activity using micellar electrokinetic chromatography (MEKC) is described. The method is based on the direct determination of citrulline formed upon enzymatic reaction. Using a background electrolyte consisting of 35 mM sodium tetraborate, pH 9.3, containing 65 mM sodium dodecyl sulfate (SDS), the peak of citrulline in the electropherogram was easily identified and integrated. This allowed us to determine the rate of formation of the reaction product and to calculate the kinetic parameter Km of the OTC-ase investigated. The capillary electrophoretic method developed was applied to the determination of OTC-ase activity in plasma samples for citrulline in the nanogram range.

Threonine 82 in the regulatory chain is important for nucleotide affinity and for the allosteric stabilization of Escherichia coli aspartate transcarbamoylase

The three-dimensional structure of Escherichia coli aspartate transcarbamoylase complexed with the allosteric effector CTP, shows an interaction between the hydroxyl of Thr-82 in the regulatory chain (Thr-82r) with the gamma-phosphate of CTP (R.P. Kosman, J.E. Gouaux, W.N. Lipscomb, Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for aspartate transcarbamoylase mutants and the mechanism of negative cooperativity, Proteins Struct. Funct. Genet. 15 (1993) 147-176). In order to determine whether the Thr-82r interaction with the gamma-phosphate of CTP is important for either binding of the nucleotide effectors or their function, site-specific mutagenesis was employed. The mutant enzyme in which Thr-82r was replaced by Ala had almost the identical maximal observed specific activity as the wild-type enzyme; however, the mutant enzyme had a significantly increased [Asp]0.5, the aspartate concentration at one-half the maximal observed specific activity, as well as slightly increased homotropic cooperativity. The mutant enzyme was also activated more by ATP and inhibited less by CTP as compared to the wild-type enzyme. In addition, the nucleotide concentration required for one-half maximal effect was increased approx. 3-fold as compared to the corresponding values for the wild-type enzyme. The maximal inhibition of the mutant enzyme, in the presence of UTP and CTP was similar to that observed for the wild-type enzyme; however, higher concentrations of the nucleotides were required to achieve this level of inhibition. The reduced affinity of CTP, UTP and ATP induced by the mutation indicates that the hydrogen bonding interaction between the gamma-phosphate of the nucleotide effector and the side-chain hydroxyl of Thr-82r is important for the binding of the nucleotide effectors to the allosteric site. Furthermore, this interaction is important for the discrimination between CTP and CDP. Finally, the greater homotropic cooperativity, greater [Asp]0.5, diminished CTP inhibition and greater ATP activation of the mutant enzyme correlates with the X-ray structure of the mutant enzyme which shows that the unligated enzyme is in an 'extreme' T-state. These findings add support to the theory that the global stabilization of the enzyme is critical for both the homotropic and heterotropic properties of aspartate transcarbamoylase.

Colorimetric determination of citrulline residues in proteins

A method is described for the direct colorimetric determination of citrulline residues in proteins based on the reaction with diacetylmonoxime in the presence of lower concentrations of sulfuric acid. The reduced sensitivity due to the lower acid concentration was overcome by the addition of ferric chloride which also contributed to the color stabilization. Insoluble proteins or proteins resulting in turbidity can be analyzed following partial hydrolysis of those with enzyme or acid. The molar absorption coefficient (epsilon) for citrulline at 464 nm was 2.8 x 10(4). The method enabled us to determine low levels of protein-bound citrulline which are beyond the limitations of conventional methods using an amino acid analyzer. We determined the citrulline contents in the cornified cells of the epidermis of newborn rats, as well as soybean trypsin inhibitor.

Aspartate transcarbamylase from the hyperthermophilic eubacterium Thermotoga maritima: fused catalytic and regulatory polypeptides form an allosteric enzyme

In the allosteric aspartate transcarbamylase (ATCase) from the hyperthermophilic eubacterium Thermotoga maritima, the catalytic and regulatory functions, which in class B ATCases are carried out by specialized polypeptides, are combined on a single type of polypeptide assembled in trimers. The ATCases from T. maritima and Treponema denticola present intriguing similarities, suggesting horizontal gene transfer.

Allosteric regulation in Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase revisited: association of concerted homotropic cooperative interactions and local heterotropic effects

The allosteric catabolic ornithine carbamoyltransferase (OTCase) from Pseudomonas aeruginosa, a dodecamer build up of four trimers of identical subunits, shows strong carbamoylphosphate homotropic co-operativity. Its activity is allosterically inhibited by spermidine and activated by AMP. Modified forms of the enzyme exhibiting substantial alterations in both homotropic and heterotropic interactions were recently obtained. We report here the first detailed kinetic characterization of homotropic and heterotropic modulations in allosteric wild-type and in engineered OTCases. Homotropic co-operativity for the saturation either by citrulline or arsenate was also observed when arsenate was utilised as an alternate substrate of the reverse reaction. Amino acid substitution of glutamate 105 by a glycine produces an enzyme devoid of homotropic interactions between the catalytic sites for carbamoylphosphate. This mutant, which is blocked in an active conformation, is still sensitive to the allosteric effector AMP, which increases affinity with respect to the substrate, carbamoylphosphate. It is also observed that homotropic co-operative interactions do not reappear in the E105G enzyme upon strong inhibition by the allosteric inhibitor of the wild-type enzyme, spermidine.Replacement of residues 34 to 101 of the native enzyme by the homologous amino acids of anabolic Escherichia coli OTCase produces a trimeric enzyme which retains reduced homotropic co-operativity. Activation by AMP and inhibition by spermidine of this chimaeric OTCase do not affect carbamoylphosphate homotropic co-operativity. AMP acts by reducing the concentration of substrate at half maximum velocity while spermidine acts in the inverse way. These observations indicate that in the two mutant forms of OTCase, homotropic and heterotropic interactions can be uncoupled and therefore must involve different molecular mechanisms. Furthermore, the results of stimulation of enzyme activity by phosphate, arsenate, pyrophosphate and phosphonoacetyl-l-ornithine on wild-type and mutant OTCases suggest that the physiological substrate phosphate, besides acting at the catalytic site, may act at an allosteric site. On the other hand, pyrophosphate and phosphonoacetyl-l-ornithine activation results exclusively from interactions of this effector with the active site residues.

Temperature effects on the allosteric responses of native and chimeric aspartate transcarbamoylases

Although structurally very similar, the aspartate transcarbamoylases (ATCase) of Serratia marcescens and Escherichia coli have distinct allosteric regulatory patterns. It has been reported that a S. marcescens chimera, SM : rS5'ec, in which five divergent residues (r93 to r97) of the regulatory polypeptide were replaced with their Escherichia coli counterparts, possessed E. coli-like regulatory characteristics. The reverse chimera EC:rS5'sm, in which the same five residues of E. coli have been replaced with their S. marcescens counterpart, lost both heterotrophic and homotropic responses. These results indicate that the r93-r97 region is critical in defining the ATCase allosteric character. Molecular modeling of the regulatory polypeptides has suggested that the replacement of the S5' beta-strand resulted in disruption of the allosteric-zinc interface. However, the structure-function relationship could be indirect, and the disruption of the interface could influence allostery by altering the global energy of the enzyme. Studies of the temperature-sensitivity of the CTP response demonstrate that it is possible to convert CTP inhibition of the SM:rS5'ec chimera at high temperature to activation below 10 degreesC. Nonetheless, the temperature response of the native S. marcescens ATCase suggests a strong entropic effect that counteracts the CTP activation. Therefore, it is suggested that the entropy component of the coupling free energy plays a significant role in the determination of both the nature and magnitude of the allosteric effect in ATCase.