Separation of the Chlorella ATP:Urea amido-lyase into two components

The urea carboxylase and allophanate hydrolase activities of urea amidolyase are functionally independent

Urea amidolyase (UAL) is a multifunctional biotin-dependent enzyme that contributes to both bacterial and fungal pathogenicity by catalyzing the ATP-dependent cleavage of urea into ammonia and CO2 . UAL is comprised of two enzymatic components: urea carboxylase (UC) and allophanate hydrolase (AH). These enzyme activities are encoded on separate but proximally related genes in prokaryotes while, in most fungi, they are encoded by a single gene that produces a fusion enzyme on a single polypeptide chain. It is unclear whether the UC and AH activities are connected through substrate channeling or other forms of direct communication. Here, we use multiple biochemical approaches to demonstrate that there is no substrate channeling or interdomain/intersubunit communication between UC and AH. Neither stable nor transient interactions can be detected between prokaryotic UC and AH and the catalytic efficiencies of UC and AH are independent of one another. Furthermore, an artificial fusion of UC and AH does not significantly alter the AH enzyme activity or catalytic efficiency. These results support the surprising functional independence of AH from UC in both the prokaryotic and fungal UAL enzymes and serve as an important reminder that the evolution of multifunctional enzymes through gene fusion events does not always correlate with enhanced catalytic function.

Genome of the halotolerant green alga Picochlorum sp. reveals strategies for thriving under fluctuating environmental conditions

An expected outcome of climate change is intensification of the global water cycle, which magnifies surface water fluxes, and consequently alters salinity patterns. It is therefore important to understand the adaptations and limits of microalgae to survive changing salinities. To this end, we sequenced the 13.5 Mbp genome of the halotolerant green alga Picochlorum SENEW3 (SE3) that was isolated from a brackish water pond subject to large seasonal salinity fluctuations. Picochlorum SE3 encodes 7367 genes, making it one of the smallest and most gene dense eukaryotic genomes known. Comparison with the pico-prasinophyte Ostreococcus tauri, a species with a limited range of salt tolerance, reveals the enrichment of transporters putatively involved in the salt stress response in Picochlorum SE3. Analysis of cultures and the protein complement highlight the metabolic flexibility of Picochlorum SE3 that encodes genes involved in urea metabolism, acetate assimilation and fermentation, acetoin production and glucose uptake, many of which form functional gene clusters. Twenty-four cases of horizontal gene transfer from bacterial sources were found in Picochlorum SE3 with these genes involved in stress adaptation including osmolyte production and growth promotion. Our results identify Picochlorum SE3 as a model for understanding microalgal adaptation to stressful, fluctuating environments.

Opinion: nickel and urease in plants: still many knowledge gaps

We propose experimental strategies to expand our understanding of the role of Ni in plants, beyond the Ni-metallocenter of urease, still the only identified Ni-containing plant enzyme. While Ni has been considered an essential mineral for plants there is a clear lack of knowledge of its involvement in metabolic steps except the urease-catalyzed conversion of urea to ammonia and bicarbonate. We argue that urease (and hence, Ni) plays an important role in optimal N-use efficiency under various N regimes by recycling urea-N, which is generated endogenously exclusively from arginase action on arginine. We further suggest that urease and arginase may connect different metabolic compartments under stress situations, and therefore may be involved in stress tolerance. To determine possible non-urease roles of Ni we call for experimental manipulation of both Ni and N availability in urease-negative mutants. Plant ureases have been shown to have defense roles, distinct from their ureolytic activity, and we call for investigation of whether Ni helps maintain a urease conformation or stability for these non-ureolytic defense roles. The beneficial effects of Ni at upper concentration limits have not been fully examined. We posit a "Ni strategy" of plants whose growth/performance is stimulated by unusual amounts of soil Ni, for defense and/or for maximal N-use efficiency. While we know little about Ni and urease roles in N metabolism and defense, virtually nothing is known about Ni roles in plant-microbial 'consortia.' And, much of what we know of Ni and urease is limited to only a few plants, e.g. soybean, potato and Arabidopsis, and we suggest studies vigorously extended to other plants.

Allophanate hydrolase of Oleomonas sagaranensis involved in an ATP-dependent degradation pathway specific to urea

The first prokaryotic urea carboxylase has previously been purified and characterized from Oleomonas sagaranensis. As the results indicated the presence of an ATP-dependent urea degradation pathway in Bacteria, the characterization of the second component of this pathway, allophanate hydrolase, was carried out. The gene encoding allophanate hydrolase was found adjacent to the urea carboxylase gene. The purified, recombinant enzyme exhibited ammonia-generating activity towards allophanate, and, together with urea carboxylase, efficiently produced ammonia from urea in an ATP-dependent manner. The substrate specificity of the enzyme was strict, and analogs of allophanate were not hydrolyzed. Moreover, although the urea carboxylase exhibited carboxylase activity towards urea, acetamide, and formamide, ammonia-releasing activity of the two enzymes combined was detected only towards urea, indicating that the pathway was specific for urea degradation.

Enzymatic characterization of a prokaryotic urea carboxylase

We identified the first prokaryotic urea carboxylase (UCA) from a member of the alpha subclass of the class Proteobacteria, Oleomonas sagaranensis. This enzyme (O. sagaranensis Uca) was composed of 1,171 amino acids, and its N-terminal region resembled the biotin carboxylase domains of various biotin-dependent carboxylases. The C-terminal region of the enzyme harbored the Met-Lys-Met motif found in biotin carboxyl carrier proteins. The primary structure of the enzyme was 45% identical to that of the urea carboxylase domain of urea amidolyase from Saccharomyces cerevisiae. O. sagaranensis Uca did not harbor the allophanate hydrolase domain found in the yeast enzyme, but a separate gene with structural similarity was found to be adjacent to the uca gene. Purified recombinant O. sagaranensis Uca displayed ATP-dependent carboxylase activity towards urea (V(max) = 21.2 micro mol mg(-1) min(-1)) but not towards acetyl coenzyme A (acetyl-CoA) and propionyl-CoA, indicating that the gene encoded a bona fide UCA and not an acetyl-CoA or propionyl-CoA carboxylase. The enzyme also exhibited high levels of activity towards acetamide and formamide. Kinetic parameters of the enzyme reaction were determined with ATP, urea, acetamide, and formamide. O. sagaranensis could grow on urea, acetamide, and formamide as sole nitrogen sources; moreover, ATP-dependent urea-degrading activity was found in cells grown with urea but not in cells grown with ammonia. The results suggest that the UCA of this organism may be involved in the assimilation of these compounds as nitrogen sources. Furthermore, orthologues of the O. sagaranensis uca gene were found to be widely distributed among Bacteria. This implies that there are two systems of urea degradation in Bacteria, a pathway catalyzed by the previously described ureases and the UCA-allophanate hydrolase pathway identified in this study.

Nickel and the metabolism of urea by Lemna paucicostata Hegelm. 6746

With urea as sole nitrogen source, the addition of 5×10(-5) M nickel sulfate to axenic cultures of Lemna paucicostata 6746 approximately doubles the rate of vegetative growth. Under a standard light-dark schedule, Ni(2+) changes the daily pattern of respiratory CO2 output on urea from one having a single daily peak to one with two daily peaks which resembles that on ammonium or nitrate as sole nitrogen source. It also increases CO2 output by as much as 3-fold on a fresh-weight basis. These data represent the first confirmation in an intact higher plant of proposals, based on enzymology and tissue culture responses, for a role of Ni(2+) in urea metabolism. Further, they indicate the possible existence of two distinct pathways of urea utilization.

Some effects of nitrogen-starvation on nitrogen and carbohydrate metabolism inAnkistrodesmus braunii

Enzymic activities have been measured in cell-free extracts from nitrogen-starved cultures ofAnkistrodesmus braunii. During ten hours of nitrogenstarvation the activities of the enzymes nitrite reductase (E.C.1.6.6.4), glutamic dehydrogenase (E.C.1.4.1.4), glutamine synthetase (E.C.6.3.1.2) and urea amidolyase (E.C.3.5.1.5) were derepressed while the activities of the enzymes malate dehydrogenase (E.C.1.1.1.37) and hexokinase (E.C.2.7.1.1) remained more or less unchanged. In contrast, the photosynthetic capacity of the nitrogen-starved cultures declined rapidly and accompanying this decline were losses in the activities of ribulose diphosphate carboxylase (E.C.4.1.1.39) and triose phosphate-NADP-dehydrogenase (E.C.1.2.1.13).

[Anabolic and catabolic enzymes of urea metabolism in a carbohydrate-utilizing strain of Candida guilliermondii]

The yeast "H" of the genus Candida guilliermondii can grow on hydrocarbons as the only source for carbon. Urea can serve as a nitrogen source for this yeast which lacks detectable urease activity. During urea metabolism ammonia has never been accumulated in the culture medium. However, transferring the yeast from complete urea-medium into an urea containing phophate-buffer, the degradation of urea continues and ammonia is accumulated as well as CO2 evolved. In cell-free extracts of the yeast urea amidolyase activity was detected in the presence of ATP, biotin and specific cations. Obviously, the synthesis of urea amidolyase is induced by urea and arginine and repressed by the catabolite ammonia. Similarly the synthesis of arginase is regulated by arginine and ammonia. The analytical data of the arginase action differ significantly in relation to the carbon source of the culture medium. Both the level of arginase and ornithine carbamyl-transferase change in a characteristic way during the batch-culture. From the lower level of arginase in relation to ornithine carbamyltransferase it can be concluded that especially in alkane-metabolizing yeast the arginine catabolism is not very intensive.

Urea amidolyase of Candida utilis. Characterization of the urea cleavage reactions

Evidence is presented that the enzymes catalyzing the three reactions involved in urea cleavage in Candida utilis, biotin carboxylation, urea carboxylation, and allophanate hydrolysis occur as a complex of enzymes. The allophanate-hydrolyzing activity could not be separated from the urea-cleaving activity using common methods of protein purification. Further, urea cleavage and allophanate hydrolysis activities are induced coordinately in cells grown on various nitrogen sources. The reactions involved in urea cleavage can be distinguished from one another on the basis of their sensitivities to (a) heat, (b) pH, and (c) chemical inhibitors. Evidence is presented for the product of the first reaction in urea cleavage, biotin carboxylation. Production of carboxylated enzyme is ATP dependent and avidin sensitive. Carboxylated enzyme is not observed in the presence of 1 mM urea.

Metabolic control of urea catabolism in Chlamydomonas reinhardi and Chlorella pyrenoidosa

In the unicellular green alga Chlamydomonas reinhardi (strain y-1), synthesis of the enzymes required for urea hydrolysis is under substrate induction control by urea and under end product repression control by ammonia. Hydrolysis of urea if effected by the sequential action of the discrete enzymes urea carboxylase and allophanate lyase, collectively called urea amidolyase. The carboxylase converts urea to allophanate in a reaction requiring biotin, adenosine 5'-triphosphate, and Mg2+. The lyase hydrolzyes allophanate to ammonium ions and bicarbonate. Neither activity is present in more than trace amounts when cultures are grown with ammonia or urea plus ammonia, or when they are starved for nitrogen for 8 h. Urea in the absence of ammonia induces both activities 10 to 100 times the basal levels. Addition of ammonia to an induced culture causes complete cessation of carboxylase accumulation and an 80% depression of lyase accumulation. Ammonia does not reduce urea uptake by repressed cells, so it does not prevent induction by the mechanism of inducer exclusion. The unicellular green alga Chlorella pyrenoidosa (strain 3 Emerson) also has discrete carboxylase and lyase enzymes, but only the carboxylase exhibits metabolic control.