Growth of Bacillus fastidiosus on glycerol and the enzymes of ammonia assimilation

Bacillus fastidiosus was able to grow on glycerol as a carbon source when allantoin or urate was used as nitrogen source. The primary assimilatory enzyme for glycerol was glycerol kinase; glycerol dehydrogenase could not be detected. The glycerol kinase activity was increased 30-fold in allantoin/glycerol-grown cells as compared to alantoin-grown cells. Under both growth conditions high levels of glutamate dehydrogenase were found. Glutamine synthetase and glutamate synthase activities could not be demonstrated, while low levels of alanine dehydrogenase were present. It is concluded that B. fastidiosus assimilates ammonia by the NADP-dependent glutamate dehydrogenase.Abbreviations GS glutamine synthetase - GOGAT glutamate synthase - GDH glutamate dehydrogenase - ADH alanine dehydrogenase     

Stimulation of growth of Bacillus fastidiosus by amino acids

Growth of Bacillus fastidiosus on allantoin is stimulated by components of rich media as was evident from a decreased generation time and an increased maximal growth yield in the presence of such media. Such a stimulation must involve various transport systems. Energy-dependent transport systems for some amino acids were demonstrated besides those for urate, allantoin and allantoate.     

Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor

Purines are a primary source of carbon and nitrogen in soil; however, their metabolism is poorly understood in Streptomyces. Using a combination of proteomics, metabolomics, and metabolic engineering, we characterized the allantoin pathway in Streptomyces coelicolor. When cells grew in glucose minimal medium with allantoin as the sole nitrogen source, quantitative proteomics identified 38 enzymes upregulated and 28 downregulated. This allowed identifying six new functional enzymes involved in allantoin metabolism in S. coelicolor. From those, using a combination of biochemical and genetic engineering tools, it was found that allantoinase (EC 3.5.2.5) and allantoicase (EC 3.5.3.4) are essential for allantoin metabolism in S. coelicolor. Metabolomics showed that under these growth conditions, there is a significant intracellular accumulation of urea and amino acids, which eventually results in urea and ammonium release into the culture medium. Antibiotic production of a urease mutant strain showed that the catabolism of allantoin, and the subsequent release of ammonium, inhibits antibiotic production. These observations link the antibiotic production impairment with an imbalance in nitrogen metabolism and provide the first evidence of an interaction between purine metabolism and antibiotic biosynthesis.     

The effect of thiourea on ureide metabolism in Neurospora crassa

The wild-type strain of Neurospora crassa Em 5297a can utilize allantoin as a sole nitrogen source. The pathway of allantoin utilization is via its conversion into allantoic acid and urea, followed by the breakdown of urea to ammonia. This is shown by the inability of the urease-less mutant, N. crassa 1229, to grow on allantoin as a sole nitrogen source and by the formation of allantoate and urea by pre-formed mycelia of this mutant. In the wild strain (Em 5297a) thiourea is tenfold more toxic on an allantoin medium than on an inorganic nitrogen medium; allantoin as well as urea counteract thiourea toxicity in the allantoin nitrogen medium. This selective toxicity of thiourea for the mould utilizing allantoin nitrogen does not, however, result in an impairment of allantoin uptake, allantoinase activity or the formation of urea from allantoin. The only process affected by thiourea is the synthesis of urease; urea antagonizes this effect of thiourea in N. crassa.     

Studies on the molecular ecology of Blastomyces dermatitidis

The microecology of Blastomyces dermatitidis, the dimorphic etiologic agentof the potentially fatal systemic fungal infection, blastomycosis, is not well defined.Blastomyces dermatitidis may occur periodically at natural sites, perhaps aided by rotting organic material, animal droppings and physical changes. Semi-quantitative growth studies of B. dermatitidis on 2% agar plates determined the ability toutilize or tolerate a variety of substrates including simple and complex molecules as carbon source, and organic and inorganic nitrogen sources. Allantoin, creatinine, quanidoacetic acid, guanidine and cysteine may be used as sole nitrogen source. Allantoin in combination with dextrose, glycerol, lichenen, celloboise and other wood by-products support growth of B. dermatitidis at room temperature. The nutritional conversion of the fungus to the yeast form at room temperature, well demonstrated on allantoin/glycerol/yeast extract media, appears to be affected by certain inorganic compounds. The organism tolerates low to moderate levels of alpha-pinene, tannic acid, shikimic acid, veratryl alcohol, vanillic acid, and polyethyleneglycol-200. There are significant differences among isolates regarding growth on various substances at 20° and 37° centigrade. It appears that a variety of wood by-products and animal waste substrates, in combination, support the growth of B. dermatitidis. Their role in the ecological niche of B. dermatitidis, and the importance of nutritional dimorphism in the natural environment warrants further investigation. This revised version was published online in June 2006 with corrections to the Cover Date.     

Mechanisms for hydrogen production by different bacteria during mixed-acid and photo-fermentation and perspectives of hydrogen production biotechnology

H₂ has a great potential as an ecologically-clean, renewable and capable fuel. It can be mainly produced via hydrogenases (Hyd) by different bacteria, especially Escherichia coli and Rhodobacter sphaeroides. The operation direction and activity of multiple Hyd enzymes in E. coli during mixed-acid fermentation might determine H₂ production; some metabolic cross-talk between Hyd enzymes is proposed. Manipulating the activity of different Hyd enzymes is an effective way to enhance H₂ production by E. coli in biotechnology. Moreover, a novel approach would be the use of glycerol as feedstock in fermentation processes leading to H₂ production. Mixed carbon (sugar and glycerol) utilization studies enlarge the kind of organic wastes used in biotechnology. During photo-fermentation under limited nitrogen conditions, H₂ production by Rh. sphaeroides is observed when carbon and nitrogen sources are supplemented. The relationship of H₂ production with H⁺ transport across the membrane and membrane-associated ATPase activity is shown. On the other hand, combination of carbon sources (succinate, malate) with different nitrogen sources (yeast extract, glutamate, glycine) as well as different metal (Fe, Ni, Mg) ions might regulate H₂ production. All these can enhance H₂ production yield by Rh. sphaeroides in biotechnology Finally, two of these bacteria might be combined to develop and consequently to optimize two stages of H₂ production biotechnology with high efficiency transformation of different organic sources.     

Novel nitrogen sources for growth of Bacillus fastidiosus and their effect on the activity of NADP-dependent glutamate dehydrogenase

Abstract Although Bacillus fastidiosus assimilates ammonium formed internally during growth on urate, allantoin or allantoate via NADP-dependent glutamate dehydrogenase (NADP-GDH), growth on exogenous ammonium as nitrogen source has not been observed. Growth on ammonium, urea and ureidoglycolate, intermediates of the urate degradative pathway, was found to occur if the mineral growth medium containing glycerol as a carbon source was supplemented with both allantoin (0.5 mM) and brain heart infusion (BHI, 0.1%, w/v) or yeast extract. Neither allantoin nor BHI supported growth alone or in combination unless ammonium was present. NADP-GDH activity appeared to be regulated only by the extracellular concentration of allantoin or allantoate. Enzyme activity was not influenced by other nitrogen sources or the intracellular ammonium concentration.     

Carbon assimilation and extracellular antigens of some yeast-like fungi

Many yeast-like fungi assimilated n-hexadecane, butylamine and putrescine as sole carbon sources. Methanol was not assimilated. This points to a physiological similarity to endomycetous, hydrocarbon-utilizing yeasts. Stephanoascus ciferrii assimilated uric acid, adenine and allantoin as sole source of carbon and nitrogen. All strains of Geotrichum candidum and many other yeast-like fungi assimilated acetoin and butan-2,3-diol. Assimilation tests for adenine, uric acid, allantoin, acetoin and butan-2,3-diol were found to be suitable for taxonomic purposes.Extracellular antigens immunologically related to those produced by Geotrichum candidum were detected in the cell-free culture liquids of several yeast-like fungi. The extracellular antigen excreted by Stephanoascus ciferrii was species-specific.     

N and C NMR determination of allantoin metabolism in developing soybean cotyledons

The metabolism of allantoin by immature cotyledons of soybean (Glycine max L. cv Elf) grown in culture was investigated using solid state ¹³C and ¹⁵N nuclear magnetic resonance. All of the nitrogens of allantoin were incorporated into protein in a manner similar to that of each other and to the amide nitrogen of glutamine. The C-2 of allantoin was not incorporated into cellular material; presumably it was lost as CO₂. About 50% of the C-5 of allantoin was incorporated into cellular material as a methylene carbon; the other 50% was presumably also lost as CO₂. The ¹³C-¹⁵N bonds of [5-¹³C;1-¹⁵N] and [2-¹³C;1,3-¹⁵N]allantoin were broken prior to the incorporation of the nitrogens into protein. These data are consistent with allantoin's degradation to two molecules of urea and one two-carbon fragment. Cotyledons grown on allantoin as a source of nitrogen accumulated 21% of the nitrogen of cotyledons grown on glutamine. Only 50% of the nitrogen of the degraded allantoin was incorporated into the cotyledon as organic nitrogen; the other 50% was recovered as NH₄⁺ in the media in which the cotyledons had been grown. The latter results suggests that the lower accumulation of nitrogen by cotyledons grown on allantoin was in part due to failure to assimilate NH₄⁺ produced from allantoin. The seed coats had a higher activity of glutamine synthetase and a higher rate of allantoin degradation than cotyledons indicating that seed coats play an important role in the assimilation and degradation of allantoin.     

Regulation of methanol metabolism in the yeast Hansenula polymorpha

A study of enzyme profiles in Hansenula polymorpha grown on various carbon substrates revealed that the synthesis of the methanol dissimilatory and assimilatory enzymes is regulated in the same way, namely by catabolite repression and induction by methanol. Mutants of H. polymorpha blocked in dihydroxyacetone (DHA) synthase (strain 70 M) or DHA kinase (strain 17 B) were unable to grow on methanol which confirmed the important role attributed to these enzymes in the biosynthetic xylulose monophosphate (XuMP) cycle. Both mutant strains were still able to metabolize methanol. In the DNA kinase-negative strain 17 B this resulted in accumulation of DHA. Although DHA kinase is thought to be involved in DHA and glycerol metabolism in methylotrophic yeasts, strain 17 B was still able to grow on glycerol at a rate similar to that of the wild type. DHA on the other hand only supported slow growth of this mutant when relatively high concentrations of this compound were provided in the medium. This slow but definite growth of strain 17 B on DHA was not based on the reversible DHA synthase reaction but on conversion of DHA into glycerol, a reaction catalyzed by DNA reductase. The subsequent metabolism of glycerol in strain 17 B and in wild type H. polymorpha, however, remains to be elucidated.Abbreviations XuMP xylulose monophosphate - DHA dihydroxyacetone - EMS ethyl methanesulphonate     

Inhibition of purine utilization by adenine in Alcaligenes eutrophus H16

With 0.5% substrate present in mineral medium, cells of Alcaligenes eutrophus H 16 were able to grow heterotrophically at the expense of guanine, hypoxanthine and xanthine, but not of adenine as sole sources of carbon and nitrogen. An increase in cell counts, however, was observed at lower adenine concentrations (0.1%). Similarly, adenine was only respired if present at low concentrations. Higher amounts of adenine were inhibitory to the utilization of adenine, guanine, hypoxanthine, xanthine, allantoin and glyoxylate, but not to that of fructose or glycerate. The adenine-dependent inhibition of adenine utilization was not overcome by the addition of thiamine, uridine or cytidine. The enzyme glyoxylate carboligase, usually formed in presence of metabolisable purines and of allantoin, was synthesized only at low adenine concentrations. Higher amounts were inhibitory even with allantoin present as additional substrate. According to these resutls, the utilization of purine derivatives and of allantoin as sources of carbon and energy is repressed by adenine in cells of A. eutrophus H 16.     

Untersuchungen zum Glyoxylsäurestoffwechsel vonBacillus fastidiosus Stamm 83

Zusammenfassung BeiBacillus fastidiosus, der Harnsäure und Allantoin über Glyoxylsäure abbaut, wurde der Glyoxylat-Stoffwechsel untersucht. Enzyme des Glycin-Serin-Weges, des Oxalat-Weges und des -Hydroxyaspartat-Weges waren in zellfreien Extrakten nicht nachweisbar. Das Enzym Glyoxylatcaboligase, welches die Synthese von Tartronsäuresemialdehyd (TSA) aus Glyoxylsäure katalysiert, war zwar in den Extrakten vorhanden,abereine nachfolgende Umsetzung von TSA über den Glycerat-Weg schien unwahrscheinlich, da keine Glyceratkinase nachgewiesen werden konnte. Allerdingswurde eine enzymatische Tautomerisierung von Enzymen, welche die Synthese von Pyruvat aus HP über Serin katalysieren,deutet darauf hin, daß die beobachtete enzymatische Umwandlung von TSA zu HP in diesem Organismus an der Synthese von C₃-Verbindungen aus Glyoxylat beteiligt ist.

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Glyoxylate metabolism was studied inBacillus fastidiosus, which is known to degrade uric acid and allantoin via glyoxylic acid. Enzymes of the glycine-serine pathway, of the oxalate pathway and of the -hydroxyaspartate pathway were not detected in cell-free extracts. Glycoxylate carboligase, which catalyzes the formation of tartronic semialdehyde (TSA) from glyoxylate was found to be present. A further utilization of TSA via the glycerate pathway appeared to be unlikely, since no glycerate kinase could be demonstrated. However, an enzymatic tautomerisation of TSA to hydroxypyruvate (HP) was observed in the extracts. Methods for the detection of this enzyme were described. The presence of enzymes, catalyzing the synthesis of pyruvate from HP via serine indicated that the observed enzymatic conversion of TSA to HP might participate in the formation of C₃-compounds from glyoxylate in this microorganism.

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Abkürzungen HP Hydroxypyruvat - TSA Tartronsäuresemialdehyd Ausug aus der Disseration von W. Braun: Untersuchungen zum Glyoxylsäurestoffwechsel und zur Substrataufnahme anBacillus fastidiosus DSM 83, Saarbrücken (1976)     

Effect of Carbon Source on Enzymes and Metabolites of Arginine Metabolism in Neurospora

The levels of enzymes and metabolites of arginine metabolism were determined in exponential cultures of Neurospora crassa grown on various carbon sources. The carbon sources decreased in effectiveness (as determined by generation times) in the following order: sucrose, acetate, glycerol, and ethanol. The basal and induced levels of the catabolic enzymes, arginase (EC 3.5.3.1) and ornithine transaminase (EC 2.6.1.13), were lower in mycelia grown on poor carbon sources. Arginase was more sensitive to variations in carbon source than was ornithine transaminase. Induction of both enzymes was sensitive to nitrogen metabolite control, but this sensitivity was reduced in mycelia grown on glycerol or ethanol. The pools of arginine and ornithine were reduced in mycelia grown in unsupplemented medium containing poor carbon sources, but the biosynthetic enzyme ornithine transcarbamylase (EC 2.1.3.3) was not derepressed. The arginine pools were similar, regardless of carbon source, in mycelia grown in arginine-supplemented medium. The ornithine pool was reduced by growth on poor carbon sources. The rate of arginine degradation was proportional to the level of arginase in both sucrose- and glycerol-grown mycelia. The distribution of arginine between cytosol and vesicles was only slightly altered by growth on glycerol instead of sucrose. The slightly smaller cytosolic arginine concentration did not appear to be sufficient to account for the alterations in basal and induced enzyme levels. The results suggest a possible carbon metabolite effect on the expression or turnover of a variety of genes for enzymes of arginine metabolism in Neurospora.     

Induction of the allantoin degradative enzymes by allophanic acid, the last intermediate of the pathway

$\text{Saccharomyces cerevisiae}$ can utilize allantoin as a sole nitrogen source by degrading it in five steps to ammonia, “CO₂”, and glyoxylate. We have previously shown that allophanic acid is the inducer of the urea carboxylase: allophanate hydrolase multienzyme complex. Since these enzymes catalyse the last two steps of allantoin degradation, experiments were performed to determine if allophanate was also the inducer of any other enzymes in the pathway. Our data demonstrate that allophanate induces synthesis of at least five of the seven purine degradative enzymes.     

Organic nitrogen of tomato waste hydrolysate enhances glucose uptake and lipid accumulation in Cunninghamella echinulata

Aims: To investigate the effect of organic nitrogen on lipogenesis during growth of Cunninghamella echinulata on tomato waste hydrolysate (TWH) media. Methods and Results: Cunninghamella echinulata grown on a TWH medium rapidly took up glucose and produced large amounts of lipids. However, when some quantities of the organic nitrogen were removed from TWH (by acid followed by alkaline precipitation of proteins) the uptake of glucose was dramatically reduced and large quantities of fungal biomass having low lipid content were produced. Nevertheless, when glycerol was used as carbon source instead of glucose, the uptake rate as well as the biomass production and the lipid accumulation processes were unaffected by the TWH organic nitrogen removal. Finally, when the fungus was grown on a glucose supplemented TWH medium that contained no assimilable organic nitrogen (after further precipitation of proteins with methanol), the produced biomass contained non-negligible quantities of lipids, although glucose uptake remained low. Lipid analysis showed that the produced lipids comprised mainly of neutral lipids, which were preferentially consumed during lipid turnover. Lipid production on the original TWH medium having glucose as carbon source was 0·48 g of lipid per gram of dry biomass, corresponding to 8·7 g of lipid per litre of growth medium. The produced lipids contained 11·7%γ-linolenic acid (GLA), hence the GLA yield was more than 1 g l⁻¹. Conclusions: Organic nitrogen compounds found in TWH favour glucose (but not glycerol) uptake and lipid accumulation in C. echinulata. Significance and Impact of the Study: Agro-industrial wastes containing organic nitrogen, such as tomato waste, are produced in vast amounts causing severe environmental problems. These wastes could be used as fermentation feedstock to produce microbial lipids.     

Purification of allantoicase fromPseudomonas aeruginosa

Cells ofPseudomonas aeruginosa were grown in a synthetic medium containing allantoin as the sole source of carbon, nitrogen and energy. The specific activity of allantoicase in the cell-free extract amounted to 7 units/mg protein. The enzyme was purified 190 times by treatment of the extract at 72 C in the presence of Mn²⁺ions and chromatography on Ecteola-cellulose.     

Allantoin involved in species interactions with rice and other organisms in paddy soil

Allantoin (5-ureidohydantoin) plays an essential role in the assimilation, metabolism, transport, and storage of nitrogen in numerous higher plants, but its ecological implications are largely unknown. In this study allantoin was found in tissues of 11 rice (Oryza sativa) varieties tested, and its structure was characterised by X-ray diffraction analysis to confirm the fact that allantoin was actually obtained from the rice plants. Furthermore, the endogenous allantoin was exuded from the rice roots into the rhizosphere soils and had a great diversity of biological effects on associated weeds and microbes by soil interactions once released. However, allantoin levels in tissues or soils could not be distinguished between the allelopathic and non-allelopathic rice varieties. Field experiments showed that levels of allantoin released from rice varieties varied with their growth stages and reached the maximal levels at the stem elongation or panicle initiation to booting stages and then decreased dramatically. Allantoin could significantly stimulate the germination and growth of Echinochloa crus-galli and populations of soil bacteria and actinomycetes at selected test concentrations (30–500 μg/g), but had no effect on soil fungi. The half-life (t _1/2 ) of allantoin in autoclaved soil (20.2 ± 2.5 h, r ² = 0.95) was almost three-times longer than in non-autoclaved soil (7.3 ± 1.9 h, r ² = 0.92), indicating that rapid biodegradation or transformation of allantoin occurs in paddy soil. The results suggest that not only may allantoin play a role in the transport and storage of nitrogen in rice tissues but it may also participate in species interactions between rice and other organisms in paddy soil.     

Soybean ureide transporters play a critical role in nodule development,function and nitrogen export

Legumes can access atmospheric nitrogen through a symbiotic relationship with nitrogen‐fixing bacteroids that reside in root nodules. In soybean, the products of fixation are the ureides allantoin and allantoic acid, which are also the dominant long‐distance transport forms of nitrogen from nodules to the shoot. Movement of nitrogen assimilates out of the nodules occurs via the nodule vasculature; however, the molecular mechanisms for ureide export and the importance of nitrogen transport processes for nodule physiology have not been resolved. Here, we demonstrate the function of two soybean proteins – GmUPS1‐1 (XP_003516366) and GmUPS1‐2 (XP_003518768) – in allantoin and allantoic acid transport out of the nodule. Localization studies revealed the presence of both transporters in the plasma membrane, and expression in nodule cortex cells and vascular endodermis. Functional analysis in soybean showed that repression of GmUPS1‐1 and GmUPS1‐2 in nodules leads to an accumulation of ureides and decreased nitrogen partitioning to roots and shoot. It was further demonstrated that nodule development, nitrogen fixation and nodule metabolism were negatively affected in RNAi UPS1 plants. Together, we conclude that export of ureides from nodules is mediated by UPS1 proteins, and that activity of the transporters is not only essential for shoot nitrogen supply but also for nodule development and function.     

Early-blocked sporulation mutations alter expression of enzymes under carbon control in Bacillus subtilis

Summary The physiological roles of the gene subset defined by early-blocked sporulation mutations (spo0) and their second-site suppressor alleles (rvtA11 and crsA47) remain cryptic for both vegetative and sporulating Bacillus subtilis cells. To test the hypothesis that spo0 gene products affect global regulation, we assayed the levels of carbon- and nitrogen-sensitive enzymes in wild-type and spo0 strains grown in a defined minimal medium containing various carbon and nitrogen sources. All the spo0 mutations (except spo0J) affected both histidase and arabinose isomerase levels in an unexpected way: levels of both carbon-sensitive enzymes were two- to six-fold higher in spo0 strains compared to wild type, when cells were grown on the derepressing carbon sources arabinose or maltose. There was no difference in enzyme levels with glucose-grown cells, nor was there a significant difference in levels of the carbonindependent enzymes glutamine synthetase and glucose-6-phosphate dehydrogenase. This effect was not due to a slower growth rate for the spo0 mutants on the poor carbon and nitrogen sources used. The levels of carbon-sensitive enzymes were not simply correlated with sporulation ability in genetically suppressed spo0 mutants, but the rvtA and crsA suppressors each had such marked effects on wild-type growth and enzyme levels that these results were difficult to interpret. We conclude that directly or indirectly the spo0 mutations, although blocking the sporulation process, increase levels of carbon-sensitive enzymes, possibly at the level of gene expression.     

Effect of carbon source on enzymes involved in glycerol metabolism inNeurospora crassa

Specific activities of eight enzymes involved in glycerol metabolism were determined in crude extracts of three strains ofNeurospora crassa after growth on six different carbon sources. One of the strains was wild type, which grew poorly on glycerol as sole carbon source; the other two were mutant strains which were efficient glycerol utilizers. A possible basis for this greater effeciency of glycerol utilization was catabolite repression of glyceraldehyde kinase by glycerol in wild type, and two-fold higher glycerate kinase activity in the mutant strains after growth on glycerol, thus apparently allowing two routes for glyceraldehyde to enter the glycolytic pathway in the mutant strains but only one in wild type. The preferential entry of glyceraldehyde to the glycolytic pathway through glycerate was suggested by the lack of glyceraldehyde kinase in all three strains after growth on one or more of the carbon sources and the generally higher levels of aldehyde dehydrogenase and of glycerate kinase than of glyceraldehyde kinase.