The evolutionary history of the ornithine cycle as a determinant of its structure and regulation

Genetic, structural and biochemical basis of carbamoyl phosphate synthetase 1 deficiency

Carbamoyl phosphate synthetase 1 (CPS1) plays a paramount role in liver ureagenesis since it catalyzes the first and rate-limiting step of the urea cycle, the major pathway for nitrogen disposal in humans. CPS1 deficiency (CPS1D) is an autosomal recessive inborn error which leads to hyperammonemia due to mutations in the CPS1 gene, or is caused secondarily by lack of its allosteric activator NAG. Proteolytic, immunological and structural data indicate that human CPS1 resembles Escherichia coli CPS in structure, and a 3D model of CPS1 has been presented for elucidating the pathogenic role of missense mutations. Recent availability of CPS1 expression systems also can provide valuable tools for structure-function analysis and pathogenicity-testing of mutations in CPS1. In this paper, we provide a comprehensive compilation of clinical CPS1 mutations, and discuss how structural knowledge of CPS enzymes in combination with in vitro analyses can be a useful tool for diagnosis of CPS1D.

Role of Cys-1327 and Cys-1337 in redox sensitivity and allosteric monitoring in human carbamoyl phosphate synthetase

Human carbamoyl phosphate synthetase (hCPS) has evolved critical features that allow it to remove excess and potentially neurotoxic ammonia via the urea cycle, including use of only free ammonia as a nitrogen donor, a K(m) for ammonia 100-fold lower than for CPSs that also use glutamine as a nitrogen donor, and required allosteric activation by N-acetylglutamate (AGA), a sensor of excess amino acids. The recent availability of a Schizosaccharomyces pombe expression system for hCPS allowed us to utilize protein engineering approaches to elucidate the distinctive hCPS properties. Although the site of AGA interaction is not defined, it is known that the binding of AGA to CPS leads to a conformational change in which a pair of cysteine side chains become proximate and can then be selectively induced to undergo disulfide bonding. We analyzed the response of hCPS cysteine mutants to thiol-specific reagents and identified Cys-1327 and Cys-1337 as the AGA-responsive proximate cysteines. Possibly two of the features unique to urea-specific CPSs, relative to other CPSs (the conserved Cys-1327/Cys-1337 pair and the occurrence at very high concentrations in the liver mitochondrial matrix) co-evolved to provide buffering against reactive oxygen species. Reciprocal mutation analysis of Escherichia coli CPS (eCPS), creating P909C and G919C and establishing the ability of these engineered cysteine residues to share a disulfide bond, indicated an eCPS conformational change at least partly similar to the hCPS conformational change induced by AGA. These findings strongly suggested an alternative eCPS conformation relative to the single crystal conformation thus far identified.

Contrasting features of urea cycle disorders in human patients and knockout mouse models

The urea cycle exists for the removal of excess nitrogen from the body. Six separate enzymes comprise the urea cycle, and a deficiency in any one of them causes a urea cycle disorder (UCD) in humans. Arginase is the only urea cycle enzyme with an alternate isoform, though no known human disorder currently exists due to a deficiency in the second isoform. While all of the UCDs usually present with hyperammonemia in the first few days to months of life, most disorders are distinguished by a characteristic profile of plasma amino acid alterations that can be utilized for diagnosis. While enzyme assay is possible, an analysis of the underlying mutation is preferable for an accurate diagnosis. Mouse models for each of the urea cycle disorders exist (with the exception of NAGS deficiency), and for almost all of them, their clinical and biochemical phenotypes rather closely resemble the phenotypes seen in human patients. Consequently, all of the current mouse models are highly useful for future research into novel pharmacological and dietary treatments and gene therapy protocols for the management of urea cycle disorders.

Gain of glutaminase function in mutants of the ammonia-specific frog carbamoyl phosphate synthetase

Depending on their physiological role, carbamoyl phosphate synthetases (CPSs) use either glutamine or free ammonia as the nitrogen donor for carbamoyl phosphate synthesis. Sequence analysis of known CPSs indicates that, regardless of whether they are ammonia- or glutamine-specific, all CPSs contain the structural equivalent of a triad-type glutamine amidotransferase (GAT) domain. In ammonia-specific CPSs, such as those of rat or human, the catalytic inactivity of the GAT domain can be rationalized by the substitution of the Triad cysteine residue by serine (1). The ammonia-specific CPS of Rana catesbeiana (fCPS) presents an interesting anomaly in that, despite its retention of the entire catalytic triad (2) and almost all other residues conserved in Triad GATs, it is unable to utilize glutamine as a nitrogen-donating substrate (3). Based on our earlier work with the glutamine-utilizing E. coli CPS (eCPS), we have targeted residues Lys258 and Glu261 in the fCPS GAT domain as critical for preventing GAT function. Previously we have shown that substitution of the corresponding residues in eCPS by their fCPS counterparts (Leu --> Lys and Gln --> Glu) resulted in complete loss of GAT function in eCPS (3). To examine the role of these residues in the fCPS GAT component, we have cloned the full-length fCPS gene from R. catesbeiana liver. Here we report the first heterologous expression of an ammonia-specific CPS and show that a single mutation of the frog enzyme, K258L, yields a gain of glutaminase function.

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.

Urea: diverse functions of a 'waste' product

1. The urea cycle is essentially the simultaneous operation of two linear pathways, both primitive and widespread among animals; one is for arginine synthesis and the other is for arginine degradation to ornithine and urea. 2. All animals may have the genetic capacity to express a urea cycle and many diverse groups of animals, from flatworms to mammals, have a functional urea cycle. 3. Evolutionary changes in vertebrates of carbamylphosphate synthetase (CPS) are directed from glutamine-dependent (CPSIII) towards NH3-dependent (CPSI) ureagenesis. Invertebrates, cartilagenous fish and the coelacanth have CPSIII (i.e. glutamine-dependent), whereas lungfish, amphibians and amniote vertebrates have CPSI; the teleost Heteropneustes has CPSI-like activity. That the coelacanth has CPSIII and Heteropneustes has 'CPSI' suggests that the form of CPS may by physiologically related (CPSIII in a balancing solute role and CPSI in a terrestrial, air-breathing excretion role) rather than being phylogenetically constrained. 4. Urea is a major balancing osmolyte in marine cartilagenous fish, the coelacanth and a few amphibians and some aestivating terrestrial amphibians. It is a storage osmolyte in cocoon-forming aestivating lungfish and amphibians. 5. Urea contributes towards positive buoyancy in marine cartilagenous fish. 6. Urea functions for non-toxic N transport in ruminant and pseudoruminant mammals. 7. Urea is a major solute in the mammalian (but not avian) kidney, contributing to a renal medullary osmotic gradient; it is substantially reabsorbed by mammalian nephrons. 8. Urea is used as a preferred nitrogenous waste compared with ammonia at high ambient pNH3 or pH, with water restriction, or air breathing. 9. Urea synthesis maintains acid-base balance by the 1:1 stoichiometry of removal of HCO3- and NH4+.

Required allosteric effector site for N-acetylglutamate on carbamoyl-phosphate synthetase I

Carbamoyl-phosphate synthetase I (CPSase I) catalyzes the entry and rate-limiting step in the urea cycle, the pathway by which mammals detoxify ammonia. One facet of CPSase I regulation is a requirement for N-acetylglutamate (AGA), which induces an active enzyme conformation and does not participate directly in the chemical reaction. We have utilized labeling with carbodiimide-activated [14C]AGA to identify peptides 120-127, 234-237, 625-630, and 1351-1356 as potentially being near the binding site for AGA. Identification of peptide 1351-1356 confirms the previous demonstration (Rodriquez-Aparicio, L. B., Guadalajara, A. M., and Rubio, V.(1989) Biochemistry 28, 3070-3074) that the C-terminal region is involved in binding AGA. Identification of peptides 120-127 and 234-237 constitutes the first evidence that the N-terminal region of the synthetase is involved in ligand binding. Since peptides 631-638 and 1327-1348 have been identified near the ATP site of CPSase I (Potter, M. D., and Powers-Lee, S. G.(1992) J. Biol. Chem. 267, 2023-2031), the present finding of involvement of peptides 625-630 and 1351-1356 at an "allosteric" activator site was unexpected. The idea that portions of the AGA effector site might be derived from an ancestral glutamine substrate site via a gene duplication and diversification event was considered.

Comparative properties of arginases

Arginase is a primordial enzyme, widely distributed in the biosphere and represented in all primary kingdoms. It plays a critical role in the hepatic metabolism of most higher organisms as a cardinal component of the urea cycle. Additionally, it occurs in numerous organisms and tissues where there is no functioning urea cycle. Many extrahepatic tissues have been shown to contain a second form of arginase, closely related to the hepatic enzyme but encoded by a distinct gene or genes and involved in a host of physiological roles. A variety of functions has been proposed for the "extrahepatic" arginases over the last three decades. In recent years, interest in arginase has been stimulated by a demonstrated involvement in the metabolism of the ubiquitous and multifaceted molecule nitric oxide. Molecular biology has begun to furnish new clues to the disparate functions of arginases in different environments and organisms. Comparative studies of arginase sequences are also beginning to elucidate the comparative evolution of arginases, their molecular structures and the nature of their catalytic mechanism. Further studies have sought to clarify the involvement of arginase in human disease. This review presents an outline of the current state of arginase research by giving a comparative overview of arginases and their associated properties.

Urea synthesis in enterocytes of developing pigs

Urea synthesis from ammonia, glutamine and arginine was determined in enterocytes from newborn (0-day-old), 2-21-day-old suckling, and 29-58-day-old post-weaning pigs. Pigs were weaned at 21 days of age. Cells were incubated for 30 min at 37 degrees C in Krebs-Henseleit bicarbonate buffer (pH 7.4) containing (i) 0.5-2 mM NH4Cl plus 0.05-2 mM ornithine and 2 mM aspartate, (ii) 1-5 mM glutamine, or (iii) 0.5-2 mM arginine. In enterocytes from newborn and suckling pigs, there was no measurable synthesis of urea from ammonia, glutamine or arginine, and analysis of amino acids by a sensitive fluorimetric HPLC method revealed the formation of negligible amounts of ornithine from arginine. In contrast, in cells from post-weaning pigs, relatively large amounts of urea and ornithine were produced from ammonia, glutamine and arginine in a dose-dependent manner. To elucidate the mechanism of the developmental change of urea synthesis in pig enterocytes, the activities of urea-cycle enzymes were determined. The activities of enterocyte carbamoyl phosphate synthase I and ornithine carbamoyltransferase were lower in post-weaning pigs than in suckling ones, whereas there was no difference in arginino-succinate lyase. The activities of argininosuccinate synthase and arginase were increased by 4-fold and 50-100-fold, respectively, in enterocytes from post-weaning pigs compared with suckling pigs. The induction of arginase appears to be sufficient to account for the formation of urea from ammonia, glutamine and arginine in post-weaning pig enterocytes. These results demonstrate for the first time the presence of synthesis of urea from extracellular or intramitochondrially generated ammonia in enterocytes of post-weaning pigs. This hitherto unrecognized urea synthesis in these cells may be a first line of defence against the potential toxicity of ammonia produced by the extensive intestinal degradation of glutamine (a major fuel for enterocytes) and derived from diet and luminal micro-organisms.

Transcriptional regulation of genes for ornithine cycle enzymes

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Development of pyrroline-5-carboxylate synthase and N-acetylglutamate synthase and their changes in lactation and aging

Using newly developed assay procedures, we studied the development of pyrroline-5-carboxylate synthase (PCS) and N-acetylglutamate synthase (AGAS) activity in rat tissues. PCS in the small intestine of fetuses was 1/5 that of adults and reached an adult level as early as postnatal Day 1. The highest peak was observed at Day 14, and then activity decreased to the adult level. However, PCS in the brain was highest at birth and quickly inactivated in a few days. AGAS in the fetus small intestine was 1/3 that of adults and became higher than the adult level by 40% at Day 1 but was reduced to 1/2 that of adults at Day 3. Subsequently activity increased gradually to the adult level at Day 24. On the contrary, AGAS in the fetus liver was only 1/20 that of adults, and activity increased slowly up to 10 weeks and more. Pregnancy and lactation reduced liver AGAS markedly up to Day 8 and intestinal PCS considerably up to Day 14 after parturition. PCS in the small intestine of senescent rats was almost halved compared to young controls on a whole tissue basis. AGAS in the small intestine was also halved on a gram wet weight basis. Nonetheless the liver AGAS of 430-day-old rats was higher than that of the controls, although that of 630-day rats was lower. The results indicate that the arginine synthesizing enzymes in the small intestine are highly activated in suckling and weaning, and raise a question whether arginine remains fully dispensable in pregnancy, lactation, and senescence.