Organization of a multifunctional protein in pyrimidine biosynthesis. Analyses of active, tryptic fragments

The multifunctional protein which catalyzes the first three steps of pyrimidine biosynthesis in hamster cells can be cleaved by trypsin into enzymatically active fragments. When the fragments are separated by nondenaturing polyacrylamide gel electrophoresis, three major polypeptide bands appear. Carbamyl phosphate synthetase (EC 2.7.2.9), aspartate transcarbamylase (EC 2.1.3.2), and dihydroorotase (EC 3.5.2.3) activities are associated with 129,000-, 660,000-, and 94,000-dalton bands, respectively. Further analysis of these fragments by denaturing polyacrylamide gel electrophoresis has shown that the aspartate transcarbamylase band seen on the nondenaturing gel is actually a large aggregate of 39,000-dalton fragments and the dihydroorotase band is a dimer of 44,000-dalton fragments. The data reported here indicate that (i) this multifunctional protein is composed of three enzymatically independent domains, (ii) the sum of the molecular weights of these three domains (129,000 + 39,000 + 44,000 = 212,000) is similar to that of the undigested monomer (220,000 daltons), and (iii) a site important to the formation of the native multimeric protein is probably near the aspartate transcarbamylase domain.     

The overall synthesis of L-5,6-dihydroorotate by multienzymatic protein pyr1-3 from hamster cells. Kinetic studies, substrate channeling, and the effects of inhibitors

In mammals, a trifunctional protein (ME pyr1-32) synthesizes L-5,6-dihydroorotate in three sequential reactions catalyzed by carbamyl phosphate synthetase (EC 2.7.2.9), aspartate transcarbamylase (EC 2.1.3.2), and dihydroorotase (EC 3.5.2.3). 14C-labeled HCO3- has been used as a precursor for the synthesis of L-5,6-dihydroorotate by purified ME pyr1-3, and when this product is converted enzymatically to orotidine 5'-monophosphate, the concentrations of the two intermediates of ME pyr1-3, carbamyl phosphate, and N-carbamyl-L-aspartate, reach steady state concentrations of approximately 0.20 microM and 7.1 microM, respectively. At pH 7.4 in the presence of 0.1 mM 5-phosphoribosyl 1-pyrophosphate and 10% (v/v) glycerol, pure ME pyr1-3 has a Michaelis constant for HCO3- of 0.61 mM and a maximal specific activity of 329 pmol of L-5,6-dihydroorotate synthesized/min/microgram, equivalent to a turnover number of 65.8 mol min-1 (mol of subunit)-1. Consideration of the Km and Vmax values of aspartate transcarbamylase and dihydroorotase determined under the same conditions as the overall rate of synthesis of L-5,6-dihydroorotate by ME pyr1-3, indicates that the local concentrations of carbamyl phosphate at the active site of aspartate transcarbamylase and of N-carbamyl-L-aspartate at the dihydroorotase site must be 2.2-fold and 3.1-fold higher, respectively, than their average concentrations in the bulk solvent. Similar concentrations are predicted by calculation of steady state concentrations from ratios of the rate constants for the three activities. A high local concentration of N-carbamyl-L-aspartate at the third site is also indicated by a 3.6-fold reduction in the transient time for dihydroorotase activity from that predicted. Competition experiments performed with exogenous carbamyl phosphate and N-carbamyl-L-aspartate indicate only partial channeling of these intermediates. The inhibitory effect of N-phosphonacetyl-L-aspartate (PALA), at concentrations up to at least 2.4 microM, upon the aspartate transcarbamylase activity of ME pyr1-3 can be overcome by accumulated carbamyl phosphate. This mechanism for resistance to PALA could be manifest in cells which lack an effective phosphatase activity to hydrolyze carbamyl phosphate. L-Cysteine, a slow acting but potent inhibitor of dihydroorotase in the absence of substrates (Christopherson, R. I., and Jones, M. E. (1980) J. Biol. Chem. 255, 3358-3370), also inactivates dihydroorotate when ME pyr1-3 is synthesizing L-5,6-dihydroorotate.     

Purification of homogeneous glutamine-dependent carbamyl phosphate synthetase from ascites hepatoma cells as a complex with aspartate transcarbamylase and dihydroorotase.

Glutamine-dependent carbamyl phosphate synthetase [EC 2.7.2.9] was purified 1,300-fold from rat ascites hepatoma cells (AH 13) as a multienzyme complex with aspartate transcarbamylase[EC 2.1.3.2] and dihydroorotase[EC 3.5.2.3], using dimethyl sulfoxide, glycerol, and dithiothreitol as stabilizers. The purified complex was essentially homogeneous on agarose-acrylamide composite gel electrophoresis and analytical ultracentrifugation. Its molecular weight was estimated to be about 870,000 by sedimentation equilibrium studies. After alkylation with iodoacetamide or reduction with 0.6% dithiothreitol at 100 degrees, the complex gave a single band on polyacrylamide gel electrophoresis in sodium dodecyl sulfate in a position corresponding to a molecular weight of 210,000. These results indicate that the complex consists of four subunits of similar size.     

Biochemical genetic analysis of pyrimidine biosynthesis in mammalian cells: I. Isolation of a mutant defective in the early steps of de novo pyrimidine synthesis.

The isolation and characterization of a new mutant of Chinese hamster ovary cells is described. This mutant, Urd-A, shows an absolute requirement for exogenously added pyrimidines for growth. Complementation analysis indicates that the lesion in this mutant is recessive. Revertants can be isolated at frequencies suggesting that it is a single gene alteration. Biochemical analysis of cell-free extracts of CHO-K1 (Urd+) and Urd-A revealed that Urd-A possesses no more than 10% of wild-type levels of carbamyl phosphate synthetase (EC 2.7.2.9) activity, no more than 1% of wild-type levels of aspartate transcarbamylase (EC 1.2.3.2) activity, and undetectable levels of dihydroorotase (EC 3.5.2.3) activity. Thus, this mutant appears simultaneously to possess marked or complete deficiencies in the activities of the first three enzymes of pyrimidine biosynthesis. Activities of the other enzymes of the pathway appear normal. The use of this mutant for biochemical-genetic studies of pyrimidine biosynthesis is discussed.     

The evolutionary history of the first three enzymes in pyrimidine biosynthesis

Some metabolic pathways are nearly ubiquitous among organisms: the genes encoding the enzymes for such pathways must therefore be ancient and essential. De novo pyrimidine biosynthesis is an example of one such metabolic pathway. In animals a single protein called CAD

1 Abbreviations: CAD, trifunctional protein catalyzing the first three steps of de novo pyrimidine biosynthesis in higher eukaryotes; CPS, carbamyl phosphate synthetase domain; CPSase, carbamyl phosphate synthetase activity; ATC, aspartate transcarbamylase domain; ATCase, aspartate transcarbamylase activity; DHO, dihydroorotase domain; DHOase, dihydroorotase activity; GLN, glutaminase subdomain or subunit of carbamyl phosphate synthetase, GL Nase, glutaminase activity; SYN, synthetase subdomain or subunit of carbamyl phosphate synthetase; SYNase, synthetase activity.

carries the first three steps of this pathway. The same three enzymes in prokaryotes are associated with separate proteins. The CAD gene appears to have evolved through a process of gene duplication and DNA rearrangement, leading to an in-frame gene fusion encoding a chimeric protein. A driving force for the creation of eukaryotic genes encoding multienzymatic proteins such as CAD may be the advantage of coordinate expression of enzymes catalyzing steps in a biosynthetic pathway. The analogous structure in bacteria is the operon. Differences in the translational mechanisms of eukaryotes and prokaryotes may have dictated the different strategies used by organisms to evolve coordinately regulated genes.     

Aggregation states and catalytic properties of the multienzyme complex catalyzing the initial steps of pyrimidine biosynthesis in rat liver.

Glutamine-dependent carbamoyl-phosphate synthetase was purified about 2100-fold from the cytosol of rat liver using 30% (v/v) dimethyl sulfoxide and 5% (w/v) glycerol as stabilizers. Throughout the purification, aspartate transcarbamylase and dihydroorotase, the second and third enzymes of pyrimidine biosynthesis, were copurified with the synthetase. These three enzymes sedimented as a single peak with a sedimentation coefficient of 27 S in sucrose gradients containing the stabilizers, indicating their existence as a multienzyme complex. The aggregation states of the complex were analyzed by sucrose gradient centrifugation under conditions approximating those used for enzymatic assay and correlated with the kinetic properties of the synthetase. In the presence of 10% glycerol and 10 mM MgATP(2-) at 18 degrees, the synthetase showed high activity and the three enzymes sedimented as a single peak with a coefficient of 25 S. The three enzymes also existed as a complex with the same coefficient when 50 muM PP-ribose-P was added in place of MgATP(2-), the sedimentation coefficient of the complex shifted to 28 S, indicating alteration in its molecular shape, rather than size. With 10% glycerol alone, the complex partially dissociated and the synthetase activity appeared in three peaks with coefficients of 26, 19, and 9 S (carbamoyl-phosphate synthetases (CPSase) a, b, and c, respectively). CPSases a, b, and c, thus obtained, were all sensitive to regulation by UTP and PP-ribose-P, but they differed MgATP(2-) (5.1, 4.8, AND 1.7 mM for CPSases a and b, and the enzyme within the original complex, respectively) and in their sensitivities to effectors. These results suggest that the aggregation may modify the catalytic and regulatory properties of the synthetase; Attempts to reassociate the components were unsuccessful.     

Immunochemical analysis of the domain structure of CAD, the multifunctional protein that initiates pyrimidine biosynthesis in mammalian cells

CAD, is a multidomain polypeptide, with a molecular weight of over 200,000, that has glutamine-dependent carbamyl-phosphate synthetase, aspartate transcarbamylase, and dihydroorotase activity as well as regulatory sites that bind UTP and 5-phosphoribosyl 1-pyrophosphate. The protein thus catalyzes the first three steps of de novo pyrimidine biosynthesis and controls the activity of the pathway in higher eukaryotes. Controlled proteolysis of CAD isolated from Syrian hamster cells, cleaves the molecule into seven major proteolytic fragments that contain one or more of the functional domains. The two smallest fragments, which had molecular weights of 44,000 and 40,000, corresponded to the fully active dihydroorotase (DHO) and aspartate transcarbamylase (ATC) domains, respectively, but the larger fragments have not been previously characterized. In this study, enzymatic assays of partially fractionated digests and immunoblotting with antibodies specifically directed against the purified ATC domain, the purified dihydroorotase domain and an 80-kDa fragment of the putative carbamyl-phosphate synthetase domain established the precursor-product relationships among all of the major proteolytic fragments of CAD. These results indicate that 1) only the intact molecule had all of the functional domains, 2) a species with a molecular weight of 200,000 was produced in the first step of proteolysis which had glutamine-dependent carbamyl-phosphate synthetase and dihydroorotase activity, but neither aspartate transcarbamylase activity nor the antigenic determinants present on the isolated ATC domain, and 3) cleavage of the 200-kDa species produced a species, with a molecular mass of 150,000 which lacked both aspartate transcarbamylase and dihydroorotase domains. This 150-kDa species, containing the postulated carbamyl-phosphate synthetase, glutamine, and regulatory (UTP, 5-phosphoribosyl 1-pyrophosphate) domains, had two elastase-sensitive sites that divided this region of the polypeptide chain into 10-, 65-, and 80-kDa segments. The location of the functional sites on these segments has not yet been established. The immunochemical analysis also revealed the existence of possible precursors of the stable aspartate transcarbamylase and dihydroorotase domains, suggesting that the chain segments connecting the functional domains of CAD are extensive and that the overall size of the intact polypeptide chain has been underestimated. On the basis of these studies we have proposed a model of the domain structure of CAD.     

Purification from hamster cells of the multifunctional protein that initiates de novo synthesis of pyrimidine nucleotides.

Carbamyl-P synthetase (EC 2.7.2.9), aspartate transcarbamylase (EC 2.1.3.2), and dihydro-orotase (EC 3.5.2.3), the first three enzymes of the de novo pathway for synthesis of pyrimidine nucleotides, have been co-purified as a single oligomeric protein from a mutant line of hamster cells selected for its ability to resist N-(phosphonacetyl)-L-aspartate (PALA), a potent and specific inhibitor of aspartate transcarbamylase. All three enzymes overaccum,late in the mutant cells (Kempe, T.D., Swyryd, E.A., Bruist, M., and Stark, G.R. (1976) Cell 9, 541-550) and the oligomer represents nearly 10% of the total cellular protein. Tens of milligrams of oligomer have been purified to homogeneity by a simple and rapid procedure, with recovery of about 50% of all three activities. The pure protein contains only one size of polypeptide, Mr approximately 200,000, as revealed by electrophoresis in danaturing gels. All three enzyme activities are associated with this polypeptide, indicating that it is multifunctional. Further evidence for a multifunctional protein is provided by titration of the oligomer with radioactive PALA, which reveals that the number of PALA binding sites approximately equals the number of polypeptide chains. The isolated multifunctional protein is a mixture of trimers and hexamers.     

Synthesis and inactivation of carbamyl phosphate synthetase isozymes of Bacillus subtilis during growth and sporulation.

Pyrimidine-repressible carbamyl phosphate synthetase P was synthesized in parallel with aspartate transcarbamylase during growth of Bacillus subtilis on glucose-nutrient broth. Both enzymes were inactivated at the end of exponential growth, but at different rates and by different mechanisms. Unlike the inactivation of aspartate transcarbamylase, the inactivation of carbamyl phosphate synthetase P was not interrupted by deprivation for oxygen or in a tricarboxylic acid cycle mutant. The arginine-repressible isozyme carbamyl phosphate synthetase A was synthesized in parallel with ornithine transcarbamylase during the stationary phase under these growth conditions. Again, both enzymes were subsequently inactivated, but at different rates and by apparently different mechanisms. The inactivation of carbamyl phosphate synthetase A was not affected in a protease-deficient mutatn the inactivation of ornithine transcarbamylase was greatly slowed.     

Mapping of the gene encoding the multifunctional protein carrying out the first three steps of pyrimidine biosynthesis to human chromosome 2

Summary The CAD gene encodes a trifunctional protein that carries the activities of the first three enzymes (carbamyl phosphate synthetase II, aspartate transcarbamylase, and dihydroorotase) of de novo pyrimidine biosynthesis. Genomic fragments of the human CAD gene have been obtained by screening a human genomic library in bacteriophage lambda using a Syrian hamster cDNA clone as a probe. These human genomic clones have been used to assign the CAD gene to human chromosome 2 using in situ hybridization to human metaphase chromosomes and Southern blot hybridization analysis of DNA isolated from a panel of Chinese hamster/human hybrid cells. In situ hybridization analysis has allowed further localization of this gene to the chromosomal region 2p21-p22.     

Dissociation by elastase digestion of enzyme complex catalyzing the initial steps of pyrimidine biosynthesis in rat liver

Glutamine-dependent carbamyl phosphate synthetase of rat liver, purified about 2,100-fold, existed as a complex with aspartate transcarbamylase and dihydroorotase, the second and third enzymes of pyrimidine biosynthesis, with a sedimentation coefficient of 27 S. Treatment of this complex with pancreatic elastase caused a selective inactivation of the transcarbamylase with concomitant dissociation of the complex. The dissociated synthetase was as sensitive to allosteric effectors as the enzyme within the complex, but had a 5 times higher apparent $\text{Km}$ for MgATP^2?. This change appears to be intimately related to the release of the enzyme from the complex.     

Control of pyrimidine biosynthesis in human lymphocytes. Inhibitory effect of guanine and guanosine on induction of enzymes for pyrimidine biosynthesis de novo in phytohemagglutinin-stimulated lymphocytes.

Human peripheral lymphocytes were incubated with Phaseolus vulgaris phytohemagglutinin. The induction of glutamine-utilizing carbamyl phosphate synthetase (EC 2.7.2.5) and aspartate transcarbamylase (EC 2.1.3.2) for pyrimidine biosynthesis de novo and the induction of uridine kinase were observed as described previously (Ito, K., and Uchino, H. (1971) J. Biol. Chem. 246, 4060-4065; Ito, K., and Uchino, H. (1973) J. Biol. Chem. 248, 389-392; Lucas, Z.J. (1967) Science 156, 1237-1240). By the addition of 1 mM guanine to the culture, the induction of the former two enzymes was inhibited, while that of uridine kinase was not, and even accelerated. An increase in the rate of [14C] bicarbonate incorporation into the acid-soluble uridine nucleotides via the de novo pathway for pyrimidine biosynthesis after phytohemagglutinin stimulation was inhibited by guanine, the incorporation rate being almost at the level of the control culture without phytohemagglutinin. Guanosine had a similar effect on pyrimidine biosynthesis. The induction of the three enzymes mentioned above was completely inhibited by adenine (1 mM). Guanine and guanosine seem to have a unique inhibitory effect on the induction of glutamine-utilizing carbamyl phosphate synthetase and aspartate transcarbamylase.     

Characterization of an Autosomal Rudimentary-Shaped Wing Mutation in DROSOPHILA MELANOGASTER That Affects Pyrimidine Synthesis

A new autosomal mutation, rudimental (ral), which causes rudimentary-shaped wings in Drosophila melanogaster, has been isolated following ethyl methanesulfonate (EMS) mutagenesis. The wing phenotype of rudimental is identical to that of the X-linked rudimentary (r) mutation, which affects the first three enzymes in the pyrimidine biosynthetic pathway. The autosomal mutant maps very close to ebony (3–70.7) at 70.42 on the right arm of chromosome 3. Analysis of the enzyme activities of orotate phosphoribosyltransferase (OPRTase) and orotidylate decarboxylase (ODCase) indicates that the ral^a26a allele has less than wild-type activity for both enzymes. This result is discussed in light of the fact that the OPRTase and ODCase activities are part of an enzyme complex, as are the carbamyl phosphate synthetase (CPSase), aspartate transcarbamylase (ATCase) and dihydroorotase (DHOase) activities, which are encoded by the complex rudimentary locus. We suggest that rudimental is also a complex locus.     

DEAE paper chromatography to separate intermediates of the pyrimidine biosynthetic pathway and to assay asparatate transcarbamylase and dihydroorotase activities

A DEAE paper chromatographic method was developed to separate the six sequential intermediates on the pyrimidine biosynthetic pathway. This method has been utilized to assay aspartate transcarbamylase and dihydroorotase activities. Consequently, it can be inferred that the remaining three enzymes unique to pyrimidine biosynthesis can also be assayed in a similar manner.     

Studies on the female sterile mutant rudimentary of Drosophila melanogaster. II. An analysis of aspartate transcarbamylase and dihydroorotase activities in wild-type and rudimentary strains

The activities of the enzymes aspartate transcarbamylase (ATCase) and dihydroorotase (DHOase) were determined in adult females from a wild-type strain and from eight different alleles of the X-linked mutation rudimentary (r) of Drosophila melanogaster. The alleles chosen span the genetic map of the r locus. The characteristics of the DHOase-catalyzed reaction which converts carbamyl aspartate to dihydroorotate are briefly described. Of all of the r strains tested, only one, r ⁹, has wild-type levels of aspartate transcarbamylase and dihydroorotase activities. The other seven show either intermediate or very low levels of activity for both enzymes. The lowered ATCase and DHOase activities observed in mutants which do not map in the region of the structural gene for these enzymes are interpreted in light of recent evidence that ATCase and DHOase are part of a three-enzyme complex.This work was supported by the following grants: PHS HDO7918, BMS 74-19691, and a Basil O'Connor Starter Grant from the National Foundation-March of Dimes.     

In situ behavior of the pyrimidine pathway enzymes in Saccharomyces cerevisiae. I. Catalytic and regulatory properties of aspartate transcarbamylase

A permeabilization procedure was adapted to allow the in situ determination of aspartate transcarbamylase activity in Saccharomyces cerevisiae. Permeabilization is obtained by treating cell suspensions with small amounts of 10% toluene in absolute ethanol. After washing, the cells can be used directly in the enzyme assays. Kinetic studies of aspartate transcarbamylase (EC 2.1.3.2) in such permeabilized cells showed that apparent Km for substrates and Ki for the feedback inhibitor UTP were only slightly different from those reported using partially purified enzyme. The aspartate saturation curve is hyperbolic both in the presence and absence of UTP. The inhibition by this nucleotide is noncompetitive with respect to aspartate, decreasing both the affinity for this substrate and the maximal velocity of the reaction. The saturation curves for both substrates give parallel double reciprocal plots. The inhibition by the products is linear noncompetitive. Succinate, an aspartate analog, provokes competitive and uncompetitive inhibitions toward aspartate and carbamyl phosphate, respectively. The inhibition by phosphonacetate, a carbamyl phosphate analog, is uncompetitive and noncompetitive toward carbamyl phosphate and aspartate, respectively, but pyrophosphate inhibition is competitive toward carbamyl phosphate and noncompetitive toward aspartate. These results, as well as the effect of the transition state analog N-phosphonacetyl-L-aspartate, all exclude a random mechanism for aspartate transcarbamylase. Most of the data suggest an ordered mechanism except the substrates saturation curves, which are indicative of a ping-pong mechanism. Such a discrepancy might be related to some channeling of carbamyl phosphate between carbamyl phosphate synthetase and aspartate transcarbamylase catalytic sites.     

Overproduction of the first three enzymes of pyrimidine nucleotide biosynthesis in Drosophila cells resistant to N-phosphonacetyl-L-aspartate

Drosophila cells were treated in vitro with N-phosphonacetyl-L-aspartate (PALA) which is a specific inhibitor of aspartate transcarbamylase, the second enzyme of the pyrimidine biosynthetic pathway. By stepwise selection using increasing amounts of this inhibitor, PALA-resistant (PALAr) stable clones have been isolated. Enzymatic activities of aspartate transcarbamylase, carbamyl phosphate synthetase and dihydro-orotase, borne by the same multifunctional protein, CAD, are increased 6-12-fold in these resistant clones compared with parental cells. The aspartate transcarbamylase in PALAr cells is shown by physical, kinetic and immunological criteria to be normal. The data from immunotitration and immunoblotting experiments indicate that the increased enzyme activities result from the overproduction of CAD.