Expression of a Rhizopus oryzae lipase in Pichia pastoris under control of the nitrogen source-regulated formaldehyde dehydrogenase promoter

A Rhizopus oryzae lipase gene has been expressed in Pichia pastoris as a reporter using the formaldehyde dehydrogenase 1 promoter (PFLD1) of this organism, which has been reported to be strongly and independently induced by either methanol as sole carbon source or methylamine as sole nitrogen source. Levels of lipase expressed and secreted under the control of the PFLD1 at different induction conditions have been compared to those obtained with the commonly used alcohol oxidase 1 promoter (PAOX1) in small (shake flask) and 1l bioreactor batch cultures. PFLD1-controlled heterologous gene expression was strongly repressed by excess of either glycerol or glucose-but not sorbitol-during growth using methylamine both as sole nitrogen source and inducing substrate. Co-induction of PFLD1 with methanol and methylamine resulted in a synergistic effect on extracellular lipase expression levels. In all tested conditions, the substitution of ammonium for methylamine as carbon source provoked a clear decrease in the specific growth rate and yield of biomass per gram of carbon source. Overall, this study demonstrates that the PFLD1 promoter is at least as efficient as the PAOX1 for extracellular expression of heterologous proteins in P. pastoris bioreactor cultures and provides a first basis for the further design of methanol-free high cell density fed-batch cultivation strategies for controlled overproduction of foreign proteins in P. pastoris.     

NAD- and co-substrate (GSH or factor)-dependent formaldehyde dehydrogenases from methylotrophic microorganisms act as a class III alcohol dehydrogenase

Abstract The methylotrophic yeasts, Hansenula polymorpha and Candida boidinii , and the methylotrophic Gram-negative bacteria, Paracoccus denitrificans and Thiobacillus versutus (but not Methylophaga marina ), contain NAD/GSH-dependent formaldehyde dehydrogenase when grown on C₁-compounds. The enzymes appeared to be similar to each other and to the mammalian counterparts with respect to substrate specificity, including the ability to act as an alcohol dehydrogenase class III. The Gram-positive bacteria, Amycolatopsis methanolica and Rhodococcus erythropolis , possess NAD/Factor-dependent formaldehyde dehydrogenase when grown on C₁-compounds or on C₁-unit-containing substrates, respectively. These enzymes also exhibit alcohol dehydrogenase class III activity. Thus, like the mammalian ones, methylotrophic formaldehyde dehydrogenases show dual substrate specificity, suggesting that this is an inherent property of the enzyme.     

An inducible periplasmic blue copper protein from Paracoccus denitrificans. Purification, properties, and physiological role

When grown on methylamine as a sole carbon source, Paracoccus denitrificans synthesizes a Type I blue copper protein which mediates electron transfer between methylamine dehydrogenase and cytochrome c. This blue copper protein does not serve as an electron acceptor for methanol dehydrogenase and is not synthesized by cells grown on methanol or succinate. The blue copper protein and methylamine dehydrogenase were localized in the periplasm of P. denitrificans, whereas formate dehydrogenase was cytoplasmic. The copper protein can be purified to high yield in a single step from the periplasmic subcellular fraction prepared from P. denitrificans. The purified protein contains a single 15,000-Da polypeptide chain and one copper atom/molecule and exhibits a pI of 4.8. The oxidized form of the protein absorbs strongly at 595 nm and weakly at 464 nm. The physical and physiological properties of this protein indicate that it is not an azurin, but representative of another class of blue copper proteins.     

Transport of methylamine by Pseudomonas sp. MA.

Pseudomonas sp. MA grows on methylamines as a sole source of carbon, nitrogen, and energy. The transport of methylamine into the organism was investigated. It was found that this organism possesses an inducible transport system for methylamine having the following physical parameters: pH optimum, 7.2; temperature optimum, 30 to 35 degrees C; Km, 1 to 30 mM; Vmax, 90 to 120 nmol/min per mg (dry weight) of cells. Methylamine uptake was curtailed by azide, cyanide, and carbonyl cyanide-m-chlorophenylhydrazone; osmotic shock treatment reduced the uptake by 50%. The uptake was not effectively inhibited by ammonium ion, amino acids, or amides, but was competitively inhibited by short-chain alkylamines. Cells grown on succinate-ammonium chloride did not possess the transport system, but it could be induced in such cells by methylamine in 20 h. Cells grown with methylamine as a sole nitrogen, but not carbon, source transported methylamine at a reduced rate.     

Growth of mycobacteria on carbon monoxide and methanol

Several mycobacterial strains, such as Mycobacterium flavescens, Mycobacterium gastri, Mycobacterium neoaurum, Mycobacterium parafortuitum, Mycobacterium peregrinum, Mycobacterium phlei, Mycobacterium smegmatis, Mycobacterium tuberculosis, and Mycobacterium vaccae, were found to grow on carbon monoxide (CO) as the sole source of carbon and energy. These bacteria, except for M. tuberculosis, also utilized methanol as the sole carbon and energy source. A CO dehydrogenase (CO-DH) assay, staining by activity of CO-DH, and Western blot analysis using an antibody raised against CO-DH of Mycobacterium sp. strain JC1 (formerly Acinetobacter sp. strain JC1 [J. W. Cho, H. S. Yim, and Y. M. Kim, Kor. J. Microbiol. 23:1-8, 1985]) revealed that CO-DH is present in extracts of the bacteria prepared from cells grown on CO. Ribulose bisphosphate carboxylase/oxygenase (RubisCO) activity was also detected in extracts prepared from all cells, except M. tuberculosis, grown on CO. The mycobacteria grown on methanol, except for M. gastri, which showed hexulose phosphate synthase activity, did not exhibit activities of classic methanol dehydrogenase, hydroxypyruvate reductase, or hexulose phosphate synthase but exhibited N,N-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase and RuBisCO activities. Cells grown on methanol were also found to have dihydroxyacetone synthase. Double immunodiffusion revealed that the antigenic sites of CO-DHs, RuBisCOs, and dihydroxyacetone synthases in all mycobacteria tested are identical with those of the Mycobacterium sp. strain JC1 enzymes.     

ASSAY OPTIMIZATION AND REGULATION OF UREASE ACTIVITY IN TWO MARINE DIATOMS

An in vitro urease enzyme assay was developed for the marine diatoms Thalassiosira pseudonana Hasle et Heimdal (clone 3H) and T. weissflogii (Grunow) Fryxell et Hasle (clone Actin). This assay involves the colorimetric measurement of ammonium following the hydrolysis of urea in crude cell homogenates and it is the first assay to account for the rate of nitrogen assimilation in both species grown on urea as the sole nitrogen source. Urease activity was found to be present regardless of nitrogen source, although activities showed distinctly different patterns depending on the species examined and form of nitrogen supplied. Under nitrogen-replete conditions, urease activity in T. pseudonana was present constitutively when grown on NH₄⁺ and upregulated when grown on NO₃⁻ or urea. In nitrogen-replete T. weissflogii , urease activity was present at high constitutive levels regardless of the nitrogen source and showed no upregulation. Nitrogen starvation did not upregulate activity in either species.     

A strong nitrogen source-regulated promoter for controlled expression of foreign genes in the yeast Pichia pastoris

In methylotrophic yeasts, glutathione-dependent formaldehyde dehydrogenase (FLD) is a key enzyme required for the metabolism of methanol as a carbon source and certain alkylated amines such as methylamine as nitrogen sources. We describe the isolation and characterization of the FLD1 gene from the yeast Pichia pastoris. The gene contains a single short intron with typical yeast-splicing signals near its 5′ end, the first intron to be demonstrated in this yeast. The predicted FLD1 product (Fld1p) is a protein of 379 amino acids (approx. 40 kDa) with 71% identity to the FLD protein sequence from the n-alkane-assimilating yeast Candida maltosa and 61–65% identity with dehydrogenase class III enzymes from humans and other higher eukaryotes. Using β-lactamase as a reporter, we show that the FLD1 promoter (P_FLD1) is strongly and independently induced by either methanol as sole carbon source (with ammonium sulfate as nitrogen source) or methylamine as sole nitrogen source (with glucose as carbon source). Furthermore, with either methanol or methylamine induction, levels of β-lactamase produced under control of P_FLD1 are comparable to those obtained with the commonly used alcohol oxidase I gene promoter (P_AOX1). Thus, P_FLD1 is an attractive alternative to P_AOX1 for expression of foreign genes in P. pastoris, allowing the investigator a choice of carbon (methanol) or nitrogen source (methylamine) regulation with the same expression strain.     

An Escherichia coli S1-like ribosomal protein is immunologically conserved in Gram-negative bacteria, but not in Gram-positive bacteria

Abstract A study was made of the enzymology of primary and intermediary pathways of C₁ metabolism in three strains of non-motile obligately methylotrophic bacteria. Each uses a variant of the ribulosemonophosphate (RMP) cycle of formaldehyde fixation which involves the Entner-Doudoroff route for hexose-phosphate cleavage and transaldolase/transketolase mode of rearrangement. The organisms possess high levels of hexulose-phosphate synthase and NAD(P)-linked glucose-6-phosphate and 6-phosphogluconate dehydrogenases. In addition they contain small activities of dye-linked methanol and methylamine dehydrogenases, PMS- and NAD-linked formaldehyde and formate dehydrogenases. This indicates cyclic rather than direct oxidation of formaldehyde derived from methanol or methylamine. The tricarboxylic acid cycle is defective in 2-ketoglutarate dehydrogenase and the glyoxylate shunt is not operating because of the absence of malate synthase. Oxaloacetate is regenerated by (phosphoenol) pyruvate carboxylases. NH⁺ ₄ is assimilated mainly by glutamate dehydrogenase. The results show metabolic similarities between motile and non-motile obligate methanol and methylamine utilizers.     

Isolation and characterization of xanthine dehydrogenase from Chlamydomonas reinhardtii

Xanthine dehydrogenase (XDH, EC 1.2.1.37) of Chlamydomonas reinhardtii (Sager) 6145c wild strain has been isolated and characterized for the first time in a unicellular green alga. The enzyme has an M_r of 330 kDa, and FAD, molybdenum and iron are cofactors required for its activity as deduced from results obtained using specific inhibitors, ⁵⁹Fe-labelling experiments, activity protection by FAD, physiological responses in vivo to iron and molybdenum deficiencies in the culture medium and work with mutants lacking molybdenum cofactor. Xanthine dehydrogenase exhibited Mi-chaelian kinetics typical for a bisubstrate enzyme with apparent K_m values for NAD ⁺, hypoxanthine and xanthine of 35, 160 and 70 μ M , respectively. Under phototrophic conditions enzyme activity was repressed by ammonium, but xanthine was not required for the enzyme to be induced, since high levels of enzyme activity were found in cells grown on ammonium and transferred to either N-frec media or media containing either of the nitrogen sources adenine, urea, urate, xanthine, hypoxanthine and guanine.     

The seven NAD(H)-glutamate dehydrogenase isoenzymes exhibit similar anabolic and catabolic activities

The specific activities of aminating NADH- and deaminating NAD⁺-glutamate dehydrogenase (GDH, EC 1.4.1.2) varied considerably in crude extracts of grapevine ( Vitis vinifera L. cv. Sultanina) callus and were dependent on the nitrogen source of the culture medium. However, dialysis of the enzyme preparations resulted in a significant decrease in the deaminating GDH specific activity while the aminating activity was not affected. The presence of malate in the crude extract resulted in erroneous overestimation of the NAD⁺-GDH activity through the malate dehydrogenase reaction. Thus, in dialysed extracts, the ratio of the NADH-GDH/NAD⁺-GDH specific activities remained relatively constant irrespective of the nitrogen source. In view of this evidence, we now have modified methods for staining both the NADH-GDH and NAD⁺-GDH activities on gels in order to compare the aminating and deaminating activities of each of the 7 GDH isoenzymes. The results from the staining of NADH-GDH and NAD⁺-GDH activity of enzyme preparations from calluses revealed the same isoenzyme profile. Furthermore, separated leaf isoenzymes showed similar activity ratios and kinetic properties. These results may suggest that each one of the 7 isoenzymes have similar in vitro anabolic and catabolic activities.     

Uptake of methylamine and methanol by Pseudomonas sp. strain AM1.

The uptake of methylamine and of methanol by the facultative methylotroph Pseudomonas sp. strain AM1 was investigated. It was found that this organism possesses two uptake systems for methylamine. One of these operates when methylamine is the sole source of carbon, nitrogen, and energy. It has a Km of 1.33 X 10(-4) M and a Vmax of 67 nmol/min per mg of cells (dry weight). The other system, found when methylamine is the sole nitrogen source only, has a Km of 1.2 X 10(-5) M and a Vmax of 8.9 nmol/min per mg of cells (dry weight). Both uptake systems were severely inhibited by azide, cyanide, carbonyl cyanide-m-chlorophenyl hydrazone, and N-ethylmaleimide, but only the high-affinity system was inhibited by ammonium ions with a Ki of 7.7 mM. Both systems were susceptible to osmotic shock treatment, competitively inhibited by ethylamine, and unaffected by most amino acids. Methanol uptake showed a Km of 4.8 microM and a Vmax of 60.6 nmol/min per mg of cells (dry weight) and was not inhibited by osmotic shock treatment. Azide, cyanide, and N-ethylmaleimide curtailed uptake, but carbonyl cyanide-m-chlorophenyl hydrazone merely reduced the rate of uptake. A methanol dehydrogenase mutant, M15A, was unable to take up methanol. It is proposed that methanol diffuses into the cell where it is rapidly oxidized by methanol dehydrogenase.     

Molybdenum-dependent degradation of nicotinic acid by Bacillus sp. DSM 2923

Abstract Growth of Bacillus sp. DSM 2923 on nicotinic acid in mineral medium was dependent on the concentration of sodium molybdate added. Addition of increasing amounts of tungstate to the medium resulted in an inhibition of growth on nicotinic acid or 6-hydroxynicotinic acid as sole source of carbon and energy. Chlorate-resistant mutants were isolated which were not able to degrade nicotinic acid and 6-hydroxynicotinic acid nor to reduce nitrate. Additionally, enzyme activities of nicotinic acid dehydrogenase and 6-hydroxynicotinic acid dehydrogenase increased with increasing concentrations of molybdate (10⁻⁸ to 10⁻⁶ M) added to the medium, and decreased with increasing amounts of tungstate (10⁻⁶ to 10⁻⁵ M) in the medium.     

Enhanced polygalacturonase production by Aspergillus niger NRRL-364 grown on supplemented citrus pectin

Enhanced levels of extracellular polygalacturonase activity were obtained when Aspergillus niger NRRL-364 was grown on pectic substances as sole carbon sources in a submerged culture. Among the factors affecting enzyme production those of carbon source concentration, nitrogen source, initial pH and time of cultivation were found to be the most important ones. Under optimum growth and activity conditions yields as high as 14.5 U (measured as reducing groups) ml^-1 of growth medium were obtained, comparing favourably with those reported for fungi grown under similar conditions and used in food processes.     

Nitrogen assimilation in facultative methylotrophic bacteria

A study was done of the pathways of nitrogen assimilation in the facultative methylotrophsPseudomonas MA andPseudomonas AM1, with ammonia or methylamine as nitrogen sources and with methylamine or succinate as carbon sources. When methylamine was the sole carbon and/or nitrogen source, both organisms possessed enzymes of the glutamine synthetase/glutamate synthase pathway, but when ammonia was the nitrogen sourcePseudomonas AM1 also synthesized glutamate dehydrogenase with a pH optimum of 9.0, andPseudomonas MA elaborated both glutamate dehydrogenase (pH optimum 7.5) and alanine dehydrogenase (pH optimum 9.0). Glutamate dehydrogenase and glutamate synthase from both organisms were solely NADPH-dependent; alanine dehydrogenase was NADH-dependent. No evidence was obtained for regulation of glutamine synthetase by adenylylation in either organism, nor did glutamine synthetase appear to regulate glutamate dehydrogenase synthesis.     

Effect of a constant supply of different nitrogen sources on protein and carbohydrate content and enzyme activities of Anabaena variabilis cells

The effect of the nitrogen source on carbohydrate and protein contents and on several enzymatic activities involved in the carbon and nitrogen metabolism was studied in Anabaena variabilis ATCC 29413 cells grown under a constant supply of either N, NO⁻₃ or NH⁺₄ at different concentrations. An enhancement of protein content accompanied by a parallel decrease of carbohydrates was observed with increasing NO⁻₃ or NH⁺₄ concentrations in the medium. In cultures containing 0.1 m M NO⁻₃ or 0.1 m M NH⁺₄ nitrogenase (EC 1.18.6.1) activity was 74 and 66%, respectively, of that found in N₂-grown cells. This activity was still present with 1 m M NO⁻₃ or 1 m M NH⁺₄ in the medium and even with 10 m M NO⁻₃, but it was completely inhibited by 5 m M NH⁺₄. Ferredoxin-nitrate reductase (EC 1.7.7.2) activity was detected only in NO⁻₃ grown cells and simultaneously with nitrogenase activity. Increasing concentrations of combined nitrogen in the medium, especially NH⁺₄, promoted a concomitant decline of glutamine synthetase (EC 6.3.1.2), NADP⁺-isocitrate dehydrogenase (EC 1.1.1.42), and NAD⁺-malate dehydrogenase (EC 1.1.1.37) activities, suggesting that these enzymes play an important role in the regulation of carbon-nitrogen metabolism in cyanobacteria.     

Photoassimilation of Glycolate, Glycine and Serine by Euglena gracilis

SYNOPSIS. Glycolate was readily utilized for growth by Euglena gracilis , strain Z, in the light at pH 3.8 under a variety of atmospheric conditions, including CO₂-free air and nitrogen. Glycolate did not support growth in the dark as sole carbon source; no significant uptake of glycolate was observed under these conditions. However, cells grown in the light with glycolate as sole carbon source were still capable of glycolate uptake for up to 3 hr after transfer to darkness, and glycolate was taken up by cells utilizing glucose in the dark. The energy requirement for glycolate utilization could thus be met either by light, or by the aerobic metabolism of glucose in the dark. DCMU, an inhibitor of photosystem II, inhibited photoassimilation of glycolate. In the light, but again not in the dark, glycine and serine also served as sole source of carbon under CO₂-free air, but not under nitrogen. Net release of ammonia to the medium accompanied the photoassimilation of glycine and serine. Of the several metabolicallyrelated compounds tested, only glycolate was utilized as sole carbon source in the light under "anaerobic" conditions. A lag in net chlorophyll synthesis occurred during the photoassimilation of glycolate glycine or serine. Determination of rates of photosynthetic ¹⁴CO₂ fixation confirmed that some inhibition of photosynthetic capacity had occurred in response to utilization of glycolate and related compounds.     

Effects of the source of inorganic nitrogen on C and N interaction in maize callus tissue: phosphoenolpyruvate carboxylase activity, cytosolic pH and 15N amino acids

The effect of N-source on the interaction between carbon and nitrogen metabolism was evaluated by measuring phosphoenolpyruvate carboxylase (PEPcase; EC 4.1.1.31) activity in callus tissue of maize ( Zea mays L. cv. Prisma) sub-cultured under different N-nutrition conditions: nitrate, ammonium or combinations of both. By comparison with the condition where both salts were supplied (control), nitrate as the sole N-source led to an increase in PEPcase activity. Ammonium alone gave a drastic decrease of tissue growth. Extracts from calli grown on equivalent media supplied with ¹⁵N-nitrate or ¹⁵N-ammonium were analysed by ¹⁵N-NMR. The labelling of amino acids in the NMR spectra showed that when ¹⁵NO⁻₃ was the unique N-source, ¹⁵N mainly accumulated in NδGln, Glu and Ala. With ¹⁵NH⁺₄ only the NδGln and γ-aminobutyric acid were labelled. The addition of both gave rise to labelled Gln, Asn, Glu, Asp, Ala, Val and γ-aminobutyric acid independently of the origin of the label. In vivo ³¹P-NMR allowed the cytoplasmic and vacuolar pH to be measured. The cytoplasmic pH showed an increase of approximately 0.3 units when nitrate was the sole source of nitrogen and a corresponding decrease when ammonium was added alone. Vacuolar pH decreased in both treatments. These results are discussed on the basis of the effect of the N-source on carbon metabolism. A hypothesis of PEPcase activation as due to the increase of cytoplasmic pH upon nitrate uptake is proposed.     

Biogenesis and turnover of peroxisomes involved in the concurrent oxidation of methanol and methylamine in Hansenula polymorpha

Growth of Hansenula polymorpha in shake flasks and chemostat cultures in the presence of methanol as the sole source of carbon and methylamine as the sole source of nitrogen was associated with the development of peroxisomes in the cells. The organelles were involved in the concurrent oxidation of these two compounds, since they contained both alcohol oxidase and amine oxidase, which are key enzymes in methanol and methylamine metabolism, respectively. In addition catalase was present. Peroxisomes with a completely crystalline substructure were observed in methanol-limited chemostat-grown cells. Amine oxidase probably formed an integral part of these crystalloids, whereas catalase was present in a freely diffusable form. Transfer of cells, grown in a methanol-limited chemostat in the presence of methylamine into glucose/ammonium sulphate media resulted in the loss of both alcohol oxidase and amine oxidase activity from the cells. This process was associated with degradation of the crystalline peroxisomes. However, when cells were transferred into glucose/methylamine media, amine oxidase activity only declined during 2 h after the transfer and thereafter increased again. This subsequent rise in amine oxidase activity was associated with the development of new peroxisomes in the cells in which degradation of the crystalline peroxisomes, originally present, continued. These newly formed organelles probably originated from peroxisomes which had not been affected by degradation. When in the methanollimited chemostat methylamine was replaced by ammonium sulphate, repression of the synthesis of amine oxidase was observed. However, inactivation of this enzyme or degradation of peroxisomes was not detected. The decrease of amine oxidase activity in the culture was accounted for by dilution of enzyme as a result of growth and washout.