The influence of carbon sources and morphology on nystatin production by Streptomyces noursei

Carbon source nutrition and morphology were examined during cell growth and production of nystatin by Streptomyces noursei ATCC 11455. This strain was able to utilise glucose, fructose, glycerol and soluble starch for cell growth, but failed to grow on media supplemented with galactose, xylose, maltose, sucrose, lactose and raffinose. Utilisation of glucose had a negative influence on production of nystatin independent of the specific growth rate when phosphate and ammonium was in excess. Consumption of carbon sources was related to the specific growth rate. S. noursei ATCC 11455 formed mainly mycelial clumps during cultivation, while pellet growth dominated the culture of the morphologically altered high producing mutant S. noursei NG7.19. When the pellet size increased above a critical size, cell growth and nystatin production terminated. Fluorescent staining of hyphae revealed that this coincided with loss of activity inside the core of the pellets, probably due to diffusion limitation of oxygen or other nutrients.     

Biosynthesis of the polyene macrolide antibiotic nystatin in Streptomyces noursei

The polyene macrolide antibiotic nystatin, produced commercially by the bacterium Streptomyces noursei, is an important antifungal agent used in human therapy for treatment of certain types of mycoses. Early studies on nystatin biosynthesis in S. noursei provided important information regarding the precursors utilised in nystatin biosynthesis and factors affecting antibiotic yield. New insights into the enzymology of nystatin synthesis became available after the gene cluster governing nystatin biosynthesis in S. noursei was cloned and analysed. Six large polyketide synthase proteins were implicated in the formation of the nystatin macrolactone ring, while other enzymes, such as P450 monooxygenases and glycosyltransferase, were assumed responsible for ring decoration. The latter data, supported by analysis of the polyene mixture synthesised by the nystatin producer, helped elucidate the complete nystatin biosynthetic pathway. This information has proved useful for engineered biosynthesis of novel nystatin analogues, suggesting a plausible route for the generation of potentially safer and more efficient antifungal drugs.     

Site-specific mutagenesis and domain substitutions in the loading module of the nystatin polyketide synthase,and their effects on nystatin biosynthesis in Streptomyces noursei

The loading module for the nystatin polyketide synthase (PKS) in Streptomyces noursei is represented by the NysA protein composed of a ketosynthase (KS(S)), acyltransferase, dehydratase, and an acyl carrier protein. The absolute requirement of this protein for initiation of nystatin biosynthesis was demonstrated by the in-frame deletion of the nysA gene in S. noursei. The role of the NysA KS(S) domain, however, remained unclear, since no data on the significance of the "active site" serine (Ser-170) residue in the loading modules of type I PKSs were available. Site-specific mutagenesis of Ser-170 both in the wild-type NysA and in the hybrid loading module containing malonyl-specific acyltransferase domain from the extender module had no effect on nystatin biosynthesis. A second mutation (S413N) of the NysA KS(S) domain was discovered that completely abolished the ability of the hybrids to restore nystatin biosynthesis, presumably by affecting the ability of the resulting proteins to catalyze the required substrate decarboxylation. In contrast, NysA and its Ser-170 mutants bearing the same S413N mutation were able to restore nystatin production to significant levels, probably by using acetyl-CoA as a starter unit. Together, these data suggest that the KS(S) domain of NysA differs from the KS(Q) domains found in the loading modules of several PKS type I systems in that the active site residue is not significant for its activity.     

In vivo analysis of the regulatory genes in the nystatin biosynthetic gene cluster of Streptomyces noursei ATCC 11455 reveals their differential control over antibiotic biosynthesis

Six putative regulatory genes are located at the flank of the nystatin biosynthetic gene cluster in Streptomyces noursei ATCC 11455. Gene inactivation and complementation experiments revealed that nysRI, nysRII, nysRIII, and nysRIV are necessary for efficient nystatin production, whereas no significant roles could be demonstrated for the other two regulatory genes. To determine the in vivo targets for the NysR regulators, chromosomal integration vectors with the xylE reporter gene under the control of seven putative promoter regions upstream of the nystatin structural and regulatory genes were constructed. Expression analyses of the resulting vectors in the S. noursei wild-type strain and regulatory mutants revealed that the four regulators differentially affect certain promoters. According to these analyses, genes responsible for initiation of nystatin biosynthesis and antibiotic transport were the major targets for regulation. Data from cross-complementation experiments showed that nysR genes could in some cases substitute for each other, suggesting a functional hierarchy of the regulators and implying a cascade-like mechanism of regulation of nystatin biosynthesis.     

Analysis of the mycosamine biosynthesis and attachment genes in the nystatin biosynthetic gene cluster of Streptomyces noursei ATCC 11455

The polyene macrolide antibiotic nystatin produced by Streptomyces noursei contains a deoxyaminosugar mycosamine moiety attached to the C-19 carbon of the macrolactone ring through the beta-glycosidic bond. The nystatin biosynthetic gene cluster contains three genes, nysDI, nysDII, and nysDIII, encoding enzymes with presumed roles in mycosamine biosynthesis and attachment as glycosyltransferase, aminotransferase, and GDP-mannose dehydratase, respectively. In the present study, the functions of these three genes were analyzed. The recombinant NysDIII protein was expressed in Escherichia coli and purified, and its in vitro GDP-mannose dehydratase activity was demonstrated. The nysDI and nysDII genes were inactivated individually in S. noursei, and analyses of the resulting mutants showed that both genes produced nystatinolide and 10-deoxynystatinolide as major products. Expression of the nysDI and nysDII genes in trans in the respective mutants partially restored nystatin biosynthesis in both cases, supporting the predicted roles of these two genes in mycosamine biosynthesis and attachment. Both antifungal and hemolytic activities of the purified nystatinolides were shown to be strongly reduced compared to those of nystatin, confirming the importance of the mycosamine moiety for the biological activity of nystatin.     

Characterization of the P450 monooxygenase NysL, responsible for C-10 hydroxylation during biosynthesis of the polyene macrolide antibiotic nystatin in Streptomyces noursei

The nysL gene, encoding a putative P450 monooxygenase, was identified in the nystatin biosynthetic gene cluster of Streptomyces noursei. Although it has been proposed that NysL is responsible for hydroxylation of the nystatin precursor, experimental evidence for this activity was lacking. The nysL gene was inactivated in S. noursei by gene replacement, and the resulting mutant was shown to produce 10-deoxynystatin. Purification and an in vitro activity assay for 10-deoxynystatin demonstrated its antifungal activity being equal to that of nystatin. The NysL protein was expressed heterologously in Escherichia coli as a His-tagged protein and used in an enzyme assay with 10-deoxynystatin as a substrate. The results obtained clearly demonstrated that NysL is a hydroxylase responsible for the post-polyketide synthase modification of 10-deoxynystatin at position C-10. Kinetic studies with the purified recombinant enzyme allowed determination of K(m) and k(cat) and revealed no inhibition of recombinant NysL by either the substrate or the product. These studies open the possibility for in vitro evolution of NysL aimed at changing its specificity, thereby providing new opportunities for engineered biosynthesis of novel nystatin analogues hydroxylated at alternative positions of the macrolactone ring.     

Physiological factors affecting streptomycin production by Streptomyces griseus ATCC 12475 in batch and continuous culture

Abstract Conditions of growth are described for the production of streptomycin by Streptomyces griseus ATCC 12475 using chemically defined minimal medium and complex medium. It was found using batch cultures that early synthesis of the antibiotic occurred during growth in minimal medium but was delayed until the onset of stationary phase in complex medium. This effect was independent of whether spores or vegetative cells were used as inoculum. Stability of streptomycin biosynthesis in continuous culture was dependent on dilution rate and medium employed. Cultures were highly unstable when grown on complex medium but could be maintained in steady states in continuous culture using minimal medium when the dilution rate was increased in a stepwise manner, starting at a dilution rate of 0.02 h⁻¹ (15% of μ _max). The effect of changing dilution rate on growth, streptomycin production and the level of streptomycin phosphotransferase was examined using this technique.     

Growth limiting substrate affects antibiotic production and associated metabolic fluxes in Streptomyces clavuligerus

Clavulanic acid biosynthesis by Streptomyces clavuligerus was dependent on the identity of the growth rate limiting nutrient in chemostat bioreactor culture (D=0.05 h^–1). In phosphate-limited media, a specific production rate of 3.65 mg_clav g_biomass h^–1 was observed while N-limited media supported 0.32 mg_clav g_biomass h^–1. No production was observed in C-limited media. Metabolic flux analysis suggested that changing the nutrient limitation affected the availability of the C₅ precursor. Flux through anaplerotic metabolism was consistent with this, reflecting the lower rate of utilisation of 2-oxo-glutarate from the tricarboxylic acid (TCA) cycle for glutamate and, ultimately, C₅ precursor production, when antibiotic was not produced. We propose that C-limitation restricts the capacity for anaplerotic metabolism, minimising the potential for extensive TCA-cycle derived biosynthesis (the first stage in production of the C₅ precursor). N-Limitation would restrict the availability of nitrogen for amino acid biosynthesis (the next stage). Under P-limitation neither of these restrictions would apply.     

Enhancement of geldanamycin production by pH shock in batch culture of Streptomyces hygroscopicus subsp. duamyceticus

Various sequences of pH change were applied in a batch bioreactor to investigate pH shock effects on geldanamycin production by Streptomyces hygroscopicus subsp. duamyceticus JCM4427. In the control culture where the pH was not controlled, the maximum geldanamycin concentration was 414 mg/l. With the pHS1 mode of pH shock, that is, an abrupt pH change from pH 6.5 to pH 5.0 and then being maintained at around pH 5.0 afterward, 768mg/l of geldanamycin was produced. With pHS2, in which the pH was changed sequentially from pH 6.7 to pH 5.0 and then back to pH 6.0, 429 mg/l of geldanamycin was produced. With pHS3 having a sequential pH change from pH 6.0 to pH 4.0 and then back to pH 6.5 followed by the third pH shock to pH 5.5, no geldanamycin production was observed. Considering that the productivity with pHS1 was about two-fold of that of the control culture with no pH control, we concluded that a more sophisticated manipulation of pH would further promote geldanamycin production.     

Changes in intermediate levels during batch culture of Saccharomyces cerevisiae

Summary Bakers' yeast has been grown on a medium containing 1% glucose in aerobic conditions. The fermentation exhibited five phases, lag, fermentative growth, transition, growth on ethanol and stationary phase. Samples were taken during each phase and analysed for the levels of a selection of intermediary metabolites. The levels of ATP, AMP, glucose 6-phosphate, fructose 1,6- diphosphate, 6-phosphogluconate, citrate and glyoxylate showed differences in the different phases of the fermentation and can be used as indicators of metabolic state, whereas ADP, triose phosphates, fructose 6-phosphate, 2-phosphoglycerate and oxalacetate did not show much variation and were less useful as metabolic indicators.     

Optimum autoregulator addition strategy for maximum virginiamycin production in batch culture of Streptomyces virginiae

Virginiae butanolides (VBs) are autoregulators of Streptomyces virginiae, which induce virginiamycin biosynthesis. Generally, autoregulators are synthesized by the microorganism itself during culture. Addition of chemically synthesized virginiae butanolide-C (VB-C), which is one of the VBs, can also control the induction time and the amount of virginiamycin production. The optimum concentration and shot-feeding time of VB-C for the maximum production of virginiamycins M and S were investigated in flasks and jar-fermentor batch cultures. VB-C addition later than 8 h from the start of culture induced not only virginiamycin M and S synthesis but also VB synthesis. Virginiamycin M and S production increased with the decrease of total VBs (produced VBs and added VB-C) concentration. That is, although VBs are needed to induce virginiamycin M and S synthesis, the amount of VB-C added should be such that as small an amount as possible of VBs is synthesized to achieve the maximum production of virginiamycins M and S. However, the VB-C addition earlier than 8 h from the start of culture showed no clear relationship between the amounts of VBs and virginiamycins M and S produced. In conclusion, the maximum production of virginiamycins M and S was attained by the shot addition of 5 mug/L VB-C at 8 h from the start of culture. The maximum value was about twofold that without VB-C addition. The optimum addition strategy of VB-C was confirmed by the jar-fermentor experiments. (c) 1995 John Wiley & Sons, Inc.     

Alcohol-induced switching over of metabolic flux in Streptomyces noursei JA0 3890b.

Short-chain alcohols, benzyl alcohol and Tween 20 were found capable of switching over the metabolic flux in Streptomyces noursei JA 3890b from the preference of oxidative deamination of alanine towards the reinforced acquisition of NH4+. These changes were correlated to the decrease of the ratio of saturated to olefinic fatty acids in the mycelium, suggesting that alcohols and other polar lipophilic compounds can interfere with the biosynthesis and the function of the cytoplasmic membrane in Streptomyces.     

An unexpected role for the putative 4'-phosphopantetheinyl transferase-encoding gene nysF in the regulation of nystatin biosynthesis in Streptomyces noursei ATCC 11455

The nysF gene encoding a putative 4'-phosphopantetheinyl transferase (PPTase) is located at the 5' border of the nystatin biosynthesis gene cluster in Streptomyces noursei. PPTases carry out post-translational modification of the acyl carrier protein domains on the polyketide synthases (PKS) required for their full functionality, and hence NysF was assumed to be involved in similar modification of the nystatin PKS. At the same time, DNA sequence analysis of the genomic region adjacent to the nysF gene revealed a gene cluster for a putative lantibiotic biosynthesis. This finding created some uncertainty regarding which gene cluster nysF functionally belongs to. To resolve this ambiguity, nysF was inactivated by both insertion of a kanamycin (Km) resistance marker into its coding region, and by in-frame deletion. Surprisingly, the nystatin production in both the nysF::Km(R) and DeltanysF mutants increased by ca. 60% compared to the wild-type, suggesting a negative role of nysF in the nystatin biosynthesis. The expression of xylE reporter gene under control of different promoters from the nystatin gene cluster in the DeltanysF mutant was studied. The data obtained clearly show enhanced expression of xylE from the promoters of several structural and regulatory genes in the DeltanysF mutant, implying that NysF negatively regulates the nystatin biosynthesis.     

Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli

The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.     

Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production

The filamentous fungus Aspergillus niger is an efficient host for the recombinant production of the glycosylated enzyme fructofuranosidase, a biocatalyst of commercial interest for the synthesis of pre-biotic sugars. In batch culture on a minimal glucose medium, the recombinant strain A. niger SKAn1015, expressing the fructofuranosidase encoding suc1 gene secreted 45U/mL of the target enzyme, whereas the parent wild type SKANip8 did not exhibit production. The production of the recombinant enzyme induced a significant change of in vivo fluxes in central carbon metabolism, as assessed by (13)C metabolic flux ratio analysis. Most notably, the flux redistribution enabled an elevated supply of NADPH via activation of the cytosolic pentose phosphate pathway (PPP) and mitochondrial malic enzyme, whereas the flux through energy generating TCA cycle was reduced. In addition, the overall possible flux space of fructofuranosidase producing A. niger was investigated in silico by elementary flux mode analysis. This provided theoretical flux distributions for multiple scenarios with differing production capacities. Subsequently, the measured flux changes linked to improved production performance were projected into the in silico flux space. This provided a quantitative evaluation of the achieved optimization and a priority ranked target list for further strain engineering. Interestingly, the metabolism was shifted largely towards the optimum flux pattern by sole expression of the recombinant enzyme, which seems an inherent attractive property of A. niger. Selected fluxes, however, changed contrary to the predicted optimum and thus revealed novel targets-including reactions linked to NADPH metabolism and gluconate formation.     

Anaerobic central metabolic pathways active during polyhydroxyalkanoate production in uncultured cluster 1 Defluviicoccus enriched in activated sludge communities

We report the isolation and characterization of an unusual strain of Streptococcus salivarius , 3C30, displaying both the macrolide–lincosamide–streptogramin B and the tetracycline resistance phenotypes. It harbours the mef (E), erm (B), and tet (M) genes carried by different genetic elements. The genetic element carrying mef (E), named mega, was investigated by long PCR and sequencing, while the presence of the Tn3872-like element, carrying tet (M) and erm (B), was demonstrated by sequencing of both the int-xis-Tn and the fragment between the two resistance genes. In strain 3C30 the mega element is 5388 bp in size and its nucleotide sequence is identical to that of the element described previously in S. salivarius , with the exception of a 912 bp deletion at the left end. The composite Tn3872-like element appeared to be nonconjugative while the mega element was transferred by conjugation to Streptococcus pneumoniae . It was, however, impossible to transfer it again from these transconjugants to other strains. In addition, only in the 3C30 strain did mega form circular structures, as identified by real-time PCR. In conclusion, we found a clinical strain of S. salivarius carrying both mega and Tn3872-like genetic elements. Mega is transferable by conjugation to S. pneumoniae but it is not transferable again from the transconjugants, suggesting a possible mobilization by recombinases of the coresident Tn3872-like transposon.     

Redirecting metabolic fluxes through cofactor engineering: Role of CoA-esters pool during L(-)-carnitine production by Escherichia coli

Cofactor engineering, defined as the purposeful modification of the pool of intracellular cofactors, has been demonstrated to be a very suitable strategy for the improvement of L(-)-carnitine production in Escherichia coli strains. The overexpression of CaiB (CoA-transferase) and CaiC (CoA-ligase), both enzymes involved in coenzyme A transfer and substrate activation during the bioprocess, led to an increase in L(-)-carnitine production. Under optimal concentrations of inducer and fumarate (used as electron acceptors) yields reached 10- and 50-fold, respectively, that obtained for the wild type strain. However, low levels of coenzyme A limited the activity of these two enzymes since the addition of pantothenate increased production. Growth on substrates whose assimilation yields acetyl-CoA (such as acetate or pyruvate) further inhibited L(-)-carnitine production. Interestingly, control steps in the metabolism of acetyl-CoA of E. coli were detected. The glyoxylate shunt and anaplerotic pathways limit the bioprocess since strains carrying deletions of isocitrate lyase and isocitrate dehydrogenase phosphatase/kinase yielded 20-25% more L(-)-carnitine than the control. On the other hand, the deletion of phosphotransacetylase strongly inhibited the bioprocess, suggesting that an adequate flux of acetyl-CoA and the connection of the phosphoenolpyruvate-glyoxylate cycle together with the acetate metabolism are crucial for the biotransformation.     

Changes in the cell wall composition and structure of Streptococcus pyogenes during batch culture

Changes in S. pyogenes cells in the process of batch cultivation have been studied. The composition of S. pyogenes cell walls has been studied by amino acid analysis; besides, their resistance to enzymatic hydrolysis and the electric conductivity of cell-wall lysates have been determined at different phases of the growth of S. pyogenes. The molar amino acid composition, expressed in percent, is unrelated to the growth phase, while the content of amino acids in preparations changes in the process of growth and reaches its maximum in the middle and in the end of the logarithmic phase. At the same time the electric conductivity of cell-wall lysates reaches the minimum level at these growth stages. The authors suggest that additional electrically charged compositions are formed in the cell walls at the beginning of the logarithmic and stationary phases. A considerable increase in the initial rate of cell-wall lysis with muramidase has been found to occur at the end of the logarithmic phase. This difference in the initial rate in the initial rates of lysis of S. pyogenes cell walls at different growth phases decreases after previous treatment of the cell walls with streptolytin possessing proteolytic activity. Analysis of these data leads to a conclusion on the "loose" structure of the outer protein layer of the cell wall at the end of the logarithmic phase of the growth curve.     

Enhancement of kasugamycin production by pH shock in batch cultures of Streptomyces kasugaensis

Biosynthesis of kasugamycin could be greatly enhanced by applying a nonnutritional stress of pH shock, that is, sequential pH changes from a neutral pH to an acidic condition and then back to the neutral condition. During the acidic period, cell growth decreased to nil. After recovery of the neutral condition, the cell growth resumed after a time lag concurrently with the biosynthesis of kasugamycin at a greatly enhanced rate compared with the control case without a pH shock. In a series of experiments performed to identify the optimal length of pH shock, four different lengths (6, 12, 24, and 48 h) of pH shock were applied. The best result was obtained when pH shock was applied for 24 h, with kasugamycin productivity approximately 7-fold higher than that of the control.     

Analysis of metabolic fluxes in batch and continuous cultures of Bacillus subtilis

It is well recognized that metabolic fluxes are the key variables that must be determined in order to understand metabolic regulation and patterns. However, owing to difficulties in measuring the flux values, evaluation of metabolic fluxes has not been an integral part of the most metabolic studies. Flux values for metabolites of glycolysis, tricarboxylic acid (TCA) cycle, and hexose monophosphate (HMP) pathway were obtained for batch and glucose-limited continuous cultures of Bacillus subtilis by combining the information from the stoichiometry of key biosynthetic reactions with the experimental data on concentrations of glucose and metabolic by-products, CO(2) evolution, and oxygen uptake rates. The results indicate that (1) the metabolic fluxes and energetic yield as well as the extent of flux mismatch in metabolic activity of glycolysis and the TCA cycle reactions can be accurately quantified; (2) the flux through the TCA cycle in continuous culture is much in excess of cell energetic and biosynthetic demands for precursors; (3) for the range of growth rates examined the TCA cycle flux increases almost in proportion to growth rate and is significantly repressed only at very high growth rates of batch cultures; and (4) for continuous cultures the isocitrate dehydrogenase catalyzed reaction of the TCA cycle is the major source of the reduced form of nicotinamide-adenine dinucleotide phosphate (NADPH) used in biosynthesis. (c) 1993 John Wiley & Sons, Inc.