Microbial production of riboflavin using riboflavin overproducers,Ashbya gossypii, Bacillus subtilis, andCandida famate: An overview

Kinetics of Riboflavin Production by Hyphopichia wangnamkhiaoensis under Varying Nutritional Conditions

Riboflavin, an essential vitamin for humans, is extensively used in various industries, with its global demand being met through fermentative processes. Hyphopichia wangnamkhiaoensis is a novel dimorphic yeast species capable of producing riboflavin. However, the nutritional factors affecting riboflavin production in this yeast species remain unknown. Therefore, we conducted a kinetic study on the effects of various nutritional factors-carbon and energy sources, nitrogen sources, vitamins, and amino acids-on batch riboflavin production by H. wangnamkhiaoensis. Batch experiments were performed in a bubble column bioreactor to evaluate cell growth, substrate consumption, and riboflavin production. The highest riboflavin production was obtained when the yeast growth medium was supplemented with glucose, ammonium sulfate, biotin, and glycine. Using these chemical components, along with the mineral salts from Castañeda-Agullo's culture medium, we formulated a novel, low-cost, and effective culture medium (the RGE medium) for riboflavin production by H. wangnamkhiaoensis. This medium resulted in the highest levels of riboflavin production and volumetric productivity, reaching 16.68 mg/L and 0.713 mg/L·h, respectively, within 21 h of incubation. These findings suggest that H. wangnamkhiaoensis, with its shorter incubation time, could improve the efficiency and cost-effectiveness of industrial riboflavin production, paving the way for more sustainable production methods.

RP-HPLC Separation and 1H NMR Identification of a Yellow Fluorescent Compound-Riboflavin (Vitamin B2)-Produced by the Yeast Hyphopichia wangnamkhiaoensis

The yeast Hyphopichia wangnamkhiaoensis excretes a brilliant yellow fluorescent compound into its growth culture. In this study, we isolated and identified this compound using reverse-phase high-performance liquid chromatography-diode array detector (RP-HPLC-DAD) as well as 1H NMR and UV-Vis spectroscopy. Two of the three RP-HPLC-DAD methods used successfully separated the fluorescent compound and involved (1) a double separation step with isocratic flow elution, first on a C18 column and later on a cyano column, and (2) a separation with a linear gradient elution on a phenyl column. The wavelengths of maximum absorption of the fluorescent compound-containing HPLC fractions (~224, 268, 372, and 446 nm) are in good agreement with those exhibited by flavins. The 1H NMR spectra revealed methyl (δ 2.30 and 2.40) and aromatic proton (δ 7.79 and 7.77) signals of riboflavin. The 1H NMR spectra of the samples spiked with riboflavin confirmed that the brilliant yellow fluorescent compound is riboflavin. The maximum excitation and emission wavelengths of the fluorescent compound were 448 and 528 nm, respectively, which are identical to those of riboflavin.

Cheese whey supports high riboflavin synthesis by the engineered strains of the flavinogenic yeast Candida famata

Background

Riboflavin is a precursor of FMN and FAD which act as coenzymes of numerous enzymes. Riboflavin is an important biotechnological commodity with annual market sales exceeding nine billion US dollars. It is used primarily as a component of feed premixes, a food colorant, a component of multivitamin mixtures and medicines. Currently, industrial riboflavin production uses the bacterium, Bacillus subtilis, and the filamentous fungus, Ashbya gossypii, and utilizes glucose and/or oils as carbon substrates.

Results

We studied riboflavin biosynthesis in the flavinogenic yeast Candida famata that is a genetically stable riboflavin overproducer. Here it was found that the wild type C. famata is characterized by robust growth on lactose and cheese whey and the engineered strains also overproduce riboflavin on whey. The riboflavin synthesis on whey was close to that obtained on glucose. To further enhance riboflavin production on whey, the gene of the transcription activator SEF1 was expressed under control of the lactose-induced promoter of the native β-galactosidase gene LAC4. These transformants produced elevated amounts of riboflavin on lactose and especially on whey. The strain with additional overexpression of gene RIB6 involved in conversion of ribulose-5-phosphate to riboflavin precursor had the highest titer of accumulated riboflavin in flasks during cultivation on whey. Activation of riboflavin synthesis was also obtained after overexpression of the GND1 gene that is involved in the synthesis of the riboflavin precursor ribulose-5-phosphate. The best engineered strains accumulated 2.5 g of riboflavin/L on whey supplemented only with (NH₄)₂SO₄ during batch cultivation in bioreactor with high yield (more than 300 mg/g dry cell weight). The use of concentrated whey inhibited growth of wild-type and engineered strains of C. famata, so the mutants tolerant to concentrated whey were isolated.

Conclusions

Our data show that the waste of dairy industry is a promising substrate for riboflavin production by C. famata. Possibilities for using the engineered strains of C. famata to produce high-value commodity (riboflavin) from whey are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01888-0.

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods

Riboflavin-producing lactic acid bacteria represent a promising and cost-effective strategy for food biofortification, but production levels are typically insufficient to support daily human requirements. In this study, we describe the novel human isolate Limosilactobacillus reuteri AMBV339 as a strong food biofortification candidate. This strain shows a high natural riboflavin (vitamin B2) overproduction of 18.36 μg/ml, biomass production up to 6 × 10¹⁰ colony-forming units/ml (in the typical range of model lactobacilli), and pH-lowering capacities to a pH as low as 4.03 in common plant-based (coconut, soy, and oat) and cow milk beverages when cultured up to 72 h at 37°C. These properties were especially pronounced in coconut beverage and butter milk fermentations, and were sustained in co-culture with the model starter Streptococcus thermophilus. Furthermore, L. reuteri AMBV339 grown in laboratory media or in a coconut beverage survived in gastric juice and in a simulated gastrointestinal dialysis model with colon phase (GIDM-colon system) inoculated with fecal material from a healthy volunteer. Passive transport of L. reuteri AMBV339-produced riboflavin occurred in the small intestinal and colon stage of the GIDM system, and active transport via intestinal epithelial Caco-2 monolayers was also demonstrated. L. reuteri AMBV339 did not cause fecal microbiome perturbations in the GIDM-colon system and inhibited enteric bacterial pathogens in vitro. Taken together, our data suggests that L. reuteri AMBV339 represents a promising candidate to provide riboflavin fortification of plant-based and dairy foods, and has a high application potential in the human gastrointestinal tract.

Occurrence of phenotypic variation in Paenibacillus polymyxa E681 associated with sporulation and carbohydrate metabolism

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We report phenotypic variation in P. polymyxa E681 occurred when grown on media.

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F-type exhibited faster cell growth than B-type after utilization of carbon sources.

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2-DE identified proteins involved in various metabolic activities.

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The motility is mediated via the downregulation of sporulation and flagella production.

We report the phenotypic variation in Paenibacillus polymyxa E681 (E681), a plant growth-promoting rhizobacterium (PGPR) isolated from a winter barley root in Korea. Phenotypic variation (F-type) occurred when E681 (B-type) was grown in the media, and F-type was generated from B-type. B- and F-types were characterized by their morphological, Biolog, and GC-MIDI analyses. F-type cells altered the original biological capacity of B-type cells on endospore and flagella formation, changes in pH in culture, and carbon utilization. In growth curve analysis, B-type variants recovered bacterial growth as the variation occurred after the decline phase, but F-type variants did not. To determine this cause, we conducted comparative proteome analysis between B- and F-types using two-dimensional gel electrophoresis (2-DE). Of the identified proteins, 47% were involved in glycolysis and other metabolic pathways associated with carbohydrate metabolism. Therefore, our findings provide new knowledge on the mechanism of phenotypic variation and insights into agricultural biotechnology.

Chromogenicity of aerobic spore-forming bacteria of the Bacillaceae family isolated from different ecological niches and physiographic zones

To determine the distribution patterns of pigmented bacteria of the Bacilaceae family in different physiographic zones and ecological niches, we recovered 787 isolates from 185 environmental samples (including the areas with radiation pollution). Among the strains obtained, 149 pigmented representatives were detected, which synthesized intracellular and extracellular pigments of yellow, red, pink, and dark colors. In compliance with physiological, biochemical, and chemotaxonomic features, the isolates were identified as 7 species of the Bacilaceae family. We demonstrated that the ability to synthesize pigments significantly depended on the culture medium composition. According to the color of the colonies, the absorption spectra of pigment extracts, their physicochemical properties, and the implementation of several qualitative tests, the pigmented isolates were divided into ten groups. The relative number of pigmented strains in the physiographic zone was consistent with the total level of solar radiation for the year. Most pigmented members of the Bacillaceae family were recovered from deserts and semi-deserts, and fewest of them originated from mixed forests. We show that among the studied ecological niches, pigmented strains were most often isolated from the phyllosphere and aquatic environment and least often from soils. However, the isolates from soils and aquatic environments exhibited a greater diversity of pigmentation, and a lesser variety of colored strains was obtained from the phyllosphere and the gastrointestinal tract of animals. We established that the quantitative and qualitative composition of pigmented isolates from the areas with radiation contamination differed significantly from those coming from the natural radiation background.

Co-Overexpression of RIB1 and RIB6 Increases Riboflavin Production in the Yeast Candida famata

Riboflavin or vitamin B2 is a water-soluble vitamin and a precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which play a key role as enzyme cofactors in energy metabolism. Candida famata yeast is a promising producer of riboflavin, as it belongs to the group of so-called flavinogenic yeasts, capable of riboflavin oversynthesis under conditions of iron starvation. The role of the particular structural genes in the limitation of riboflavin oversynthesis is not known. To study the impact of overexpression of the structural genes of riboflavin synthesis on riboflavin production, a set of plasmids containing genes RIB1, RIB6, and RIB7 in different combinations was constructed. The transformants of the wild-type strain of C. famata, as well as riboflavin overproducer, were obtained, and the synthesis of riboflavin was studied. It was found that overexpression of RIB1 and RIB6 genes coding for enzymes GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone-4-phosphate synthase, which catalase the initial steps of riboflavin synthesis, elevated riboflavin production by 13–28% relative to the parental riboflavin-overproducing strains.

Using fermentation waste of ethanol-producing yeast for bacterial riboflavin production and recycling of spent bacterial mass for enhancing the growth of oily plants

AIM

This study aims to use fermentation waste of ethanol production (solid and liquid) for riboflavin and recycling of bacterial biomass as biofertilizers to enhance the growth of some oily crop plants.

METHODS AND RESULTS

Out of ten yeast isolates from fresh milk, Clavispora lusitaniae ASU 33 (MN583181) was able to ferment different concentrations of glucose (2.5, 5, 7.5, 10, 15, and 20 %) into ethanol with high efficiency at 10%. Among seven non-Lactobacillus bacterial isolates recovered from cheese samples, two bacterial isolates Bacillus subtlis-SR2 (MT002768) and Novosphingobium panipatense-SR3 (MT002778) were selected for their high riboflavin production. Different media (control medium, fermentation waste medium, and a mixture of the fermentation waste medium and control medium (1:1)) were used for riboflavin production. These media were inoculated by a single or mixture of B. subtlis-SR2, N. panipatense-SR3. The addition of the waste medium of ethanol production to the control medium (1:1) had a stimulatory effect on riboflavin production whether inoculated either with a single strain or mixture of B. subtlis-SR2, N. panipatense-SR3. A mixture of fermentation waste and control media inoculated with N. panipatense produced a high riboflavin yield in comparison with other media. Inoculation of Zea mays and Ocimum basilicum plants either with the bacterial biomass waste of riboflavin production (B. subtlis or N. panipatense or a mixture of B. subtlis and N. panipatense) shows a stimulatory effect on the plant growth in comparison with control (uninoculated plants).

CONCLUSIONS

These results demonstrate the possibility of minimizing the cost of riboflavin and biofertilizer manufacturing via interlinking ethanol and riboflavin with the biofertilizer production technology.

SIGNIFICANCE AND IMPACT OF STUDY

This study outlines methods of evaluating the strength of spent media by applying procedures developed in the vitamins production industries. Furthermore, bacterial biomass waste can act as an environmentally friendly alternative for agrochemicals.

Cell-based influenza vaccine: current production, halal status assessment, and recommendations towards Islamic-compliant manufacturing

Influenza virus is a life-threatening pathogen that infects millions of people every year, with annual mortality in the hundreds of thousands. The scenario for controlling infection has worsened with increasing numbers of vaccine hesitancy cases reported worldwide due to objections on safety, religious and other grounds. Uses of haram (impermissible) and mashbooh (doubtful) ingredients in vaccine production has raised doubts among Muslim consumers and consequently stimulated serious vaccine hesitancy. To address this major problem, we have reviewed and recommended some alternatives appropriate for manufacturing cell-based influenza vaccine which comply with Islamic laws and consumers' needs. Intensive assessments of current influenza vaccine production in both scientific and Islamic views have led to the identification of four main ingredients deemed impermissible in novel sharia-compliant (approved by Islamic laws) vaccine manufacturing. Only some of these impermissible components could be replaced with halal (permissible) alternatives, while others remain impermissible due to unavailability and unsuitability.

Overexpression of Riboflavin Excretase Enhances Riboflavin Production in the Yeast Candida famata

Many microorganisms are capable of riboflavin oversynthesis and accumulation in a medium, suggesting that they efficiently excrete riboflavin. The mechanisms of riboflavin efflux in microorganisms remain elusive. Candida famata are representatives of a group of so-called flavinogenic yeast species that overproduce riboflavin (vitamin B₂) in response to iron limitation. The riboflavin overproducers of this yeast species have been obtained by classical mutagenesis and metabolic engineering. Overproduced riboflavin accumulates in the cultural medium rather than in the cells suggesting existence of the special mechanisms involved in riboflavin excretion. The appropriate protein and gene have not been identified in yeasts till recently. At the same time, the gene BCRP (breast cancer resistance protein) has been identified in mammal mammary glands. Several homologs of the mammal BCRP gene encoding putative riboflavin efflux protein (excretase) were identified in the flavinogenic yeasts Debaryomyces hansenii and C. famata. Here we evaluate the yeast homologs of BCRP with respect to improvement of a riboflavin production by C. famata. The closest homologs from D. hansenii or C. famata were expressed under the control of TEF1 promoter of these yeasts in the wild-type and riboflavin-overproducing strains of C. famata. Resulted transformants overexpressed the corresponding genes (designated as DhRFE and CfRFE) and produced 1.4- to 6-fold more riboflavin as compared to the corresponding parental strains. They also were characterized by overexpression of RIB1 and RIB6 genes which encode the first and the last structural enzymes of riboflavin synthesis and exhibited elevated specific activity of GTP cyclohydrolase II. Thus, overexpression of yeast homolog of mammal gene BCRP may be useful to increase the riboflavin yield in a riboflavin production process using a recombinant overproducing C. famata strain or other flavinogenic microorganisms.

Nitrogen, Amino Acids, and Carbon as Control Factors of Riboflavin Production by Novosphingobium panipatense-SR3 (MT002778)

By increasing the environmental pollution, crop losses, and side effects of chemically synthesized vitamins; new vitamin sources should be included. Through this study, we introduce novel riboflavin bacterial producer Novosphingobium panipatense-SR3 (MT002778) and tested various nutritional factors with interactions effects on the production abilities. Yeast extract, maltose, and glycine were the best nitrogen, carbon, and amino acid sources for enhancing the production, respectively. The interaction between the previous factors with three concentrations of each (+, 0, -) studied statistically using Box-Behnken statistical quadric design 13- run. The perfect interaction increases the production to 497.12 mg/l (predicted 489.45 mg/l) using 30 g/l maltose, 10 g/l yeast extract, and 1 g/l glycine. The F and P- values of the tested model of riboflavin and OD600 indicating significant results with probability ≤ 0.05. Also, the evaluating statistical parameter coefficient (R²) was 0.994 of riboflavin and 0.992 of OD600 with adjusted R² value 0.976, and 0.967, respectively, which indicated that the whole variations were explained highly by the statistical model. The novel producer proved its high riboflavin production ability especially under the optimized conditions comparing with previous producers and represents a new high-speed riboflavin producer that could utilize in the industrial process.

Production of Vitamin B2 (Riboflavin) by Microorganisms: An Overview

Riboflavin is a crucial micronutrient that is a precursor to coenzymes flavin mononucleotide and flavin adenine dinucleotide, and it is required for biochemical reactions in all living cells. For decades, one of the most important applications of riboflavin has been its global use as an animal and human nutritional supplement. Being well-informed of the latest research on riboflavin production via the fermentation process is necessary for the development of new and improved microbial strains using biotechnology and metabolic engineering techniques to increase vitamin B2 yield. In this review, we describe well-known industrial microbial producers, namely, Ashbya gossypii, Bacillus subtilis, and Candida spp. and summarize their biosynthetic pathway optimizations through genetic and metabolic engineering, combined with random chemical mutagenesis and rational medium components to increase riboflavin production.

Comparative metabolomics of Phialemonium curvatum as an omnipotent fungus cultivated on crude palm oil versus glucose

BACKGROUND

Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources.

RESULTS

Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC-MS/MS-TripleQ and GC-MS, while untargeted metabolite profiling was performed using LC-MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures.

CONCLUSIONS

Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.

Role of the regulatory genes SEF1, VMA1 and SFU1 in riboflavin synthesis in the flavinogenic yeast Candida famata (Candida flareri)

Riboflavin or vitamin B₂ is an essential dietary component for humans and animals that is the precursor of flavin coenzymes flavin mononucleotide and flavin adenine dinucleotide involved in numerous enzymatic reactions. The flavinogenic yeast Candida famata overproduces riboflavin under iron starvation; however, regulation of this process is poorly understood. Regulatory gene SEF1 encoding transcription activator has been identified. Its deletion blocks yeast ability to overproduce riboflavin under iron starvation. It was shown here that the SEF1 promoters from other flavinogenic (Candida albicans) and non-flavinogenic (Candida tropicalis) yeasts fused with the open reading frame (ORF) of SEF1 gene from C. famata are able to restore riboflavin oversynthesis in sef1Δ mutants. It is known that in the pathogenic flavinogenic yeast C. albicans, Sfu1 (GATA-type transcription factor) represses SEF1. Here, we found that deletion of SFU1 gene in wild-type C. famata leads to riboflavin oversynthesis. Moreover, it was shown that disruption of VMA1 gene (coding for vacuolar ATPase subunit A) also results in riboflavin oversynthesis in C. famata.

Modulation of the Purine Pathway for Riboflavin Production in Flavinogenic Recombinant Strain of the Yeast Candida famata

Riboflavin (vitamin B₂ ) is an indispensable nutrient for humans and animals, since it is the precursor of the essential coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), involved in variety of metabolic reactions. Riboflavin is produced on commercial scale and is used for feed and food fortification purposes, and in medicine. Until recently, the mutant strains of the flavinogenic yeast Candida famata were used in industry for riboflavin production. Guanosine triphosphate is the immediate precursor of riboflavin synthesis. Therefore, the activation of metabolic flux toward purine nucleotide biosynthesis is a promising approach to improve riboflavin production. The phosphoribosyl pyrophosphate synthetase and phosphoribosyl pyrophosphate amidotransferase are the rate limiting enzymes in purine biosynthesis. Corresponding genes PRS3 and ADE4 from yeast Debaryomyces hansenii are modified to avoid feedback inhibition and cooverexpressed on the background of a previously constructed riboflavin overproducing strain of C. famata. Constructed strain accumulates twofold more riboflavin when compared to the parental strain.

Improved riboflavin production with Ashbya gossypii from vegetable oil based on 13C metabolic network analysis with combined labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR

The fungus Ashbya gossypii is an important industrial producer of riboflavin, i.e. vitamin B₂. In order to meet the constantly increasing demands for improved production processes, it appears essential to better understand the underlying metabolic pathways of the vitamin. Here, we used a highly sophisticated set-up of parallel ¹³C tracer studies with labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR to resolve carbon fluxes in the overproducing strain A. gossypii B2 during growth and subsequent riboflavin production from vegetable oil as carbon source, yeast extract, and supplemented glycine. The studies provided a detailed picture of the underlying metabolism. Glycine was exclusively used as carbon-two donor of the vitamin's pyrimidine ring, which is part of its isoalloxazine ring structure, but did not contribute to the carbon-one metabolism due to the proven absence of a functional glycine cleavage system. The pools of serine and glycine were closely connected due to a highly reversible serine hydroxymethyltransferase. Transmembrane formate flux simulations revealed that the one-carbon metabolism displayed a severe bottleneck during initial riboflavin production, which was overcome in later phases of the cultivation by intrinsic formate accumulation. The transiently limiting carbon-one pool was successfully replenished by time-resolved feeding of small amounts of formate and serine, respectively. This increased the intracellular availability of glycine, serine, and formate and resulted in a final riboflavin titer increase of 45%.

Use of next generation sequencing data to develop a qPCR method for specific detection of EU-unauthorized genetically modified Bacillus subtilis overproducing riboflavin

Background

Recently, the presence of an unauthorized genetically modified (GM) Bacillus subtilis bacterium overproducing vitamin B2 in a feed additive was notified by the Rapid Alert System for Food and Feed (RASFF). This has demonstrated that a contamination by a GM micro-organism (GMM) may occur in feed additives and has confronted for the first time,the enforcement laboratories with this type of RASFF. As no sequence information of this GMM nor any specific detection or identification method was available, Next GenerationSequencing (NGS) was used to generate sequence information. However, NGS data analysis often requires appropriate tools, involving bioinformatics expertise which is not alwayspresent in the average enforcement laboratory. This hampers the use of this technology to rapidly obtain critical sequence information in order to be able to develop a specific qPCRdetection method.

Methods

Data generated by NGS were exploited using a simple BLAST approach. A TaqMan® qPCR method was developed and tested on isolated bacterial strains and on the feed additive directly.

Results

In this study, a very simple strategy based on the common BLAST tools that can be used by any enforcement lab without profound bioinformatics expertise, was successfully used toanalyse the B. subtilis data generated by NGS. The results were used to design and assess a new TaqMan® qPCR method, specifically detecting this GM vitamin B2 overproducing bacterium. The method complies with EU critical performance parameters for specificity, sensitivity, PCR efficiency and repeatability. The VitB2-UGM method also could detect the B. subtilis strain in genomic DNA extracted from the feed additive, without prior culturing step.

Conclusions

The proposed method, provides a crucial tool for specifically and rapidly identifying this unauthorized GM bacterium in food and feed additives by enforcement laboratories. Moreover, this work can be seen as a case study to substantiate how the use of NGS data can offer an added value to easily gain access to sequence information needed to develop qPCR methods to detect unknown andunauthorized GMO in food and feed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-015-0216-y) contains supplementary material, which is available to authorized users.

Rhizosphere ecology of lumichrome and riboflavin, two bacterial signal molecules eliciting developmental changes in plants

Lumichrome and riboflavin are novel molecules from rhizobial exudates that stimulate plant growth. Reported studies have revealed major developmental changes elicited by lumichrome at very low nanomolar concentrations (5 nM) in plants, which include early initiation of trifoliate leaves, expansion of unifoliate and trifoliate leaves, increased stem elongation and leaf area, and consequently greater biomass accumulation in monocots and dicots. But higher lumichrome concentration (50 nM) depressed root development and reduced growth of unifoliate and second trifoliate leaves. While the mechanisms remain unknown, it is possible that lumichrome released by rhizobia induced the biosynthesis of classical phytohormones that caused the observed developmental changes in plants. We also showed in earlier studies that applying either 10 nM lumichrome, 10 nM ABA, or 10 ml of infective rhizobial cells (0.2 OD600) to roots of monocots and dicots for 44 h produced identical effects, which included decreased stomatal conductance and leaf transpiration in Bambara groundnut, soybean, and maize, increased stomatal conductance and transpiration in cowpea and lupin, and elevated root respiration in maize (19% by rhizobia and 20% by lumichrome). Greater extracellular exudation of lumichrome, riboflavin and indole acetic acid by N2-fixing rhizobia over non-fixing bacteria is perceived to be an indication of their role as symbiotic signals. This is evidenced by the increased concentration of lumichrome and riboflavin in the xylem sap of cowpea and soybean plants inoculated with infective rhizobia. In fact, greater xylem concentration of lumichrome in soybean and its correspondingly increased accumulation in leaves was found to result in dramatic developmental changes than in cowpea. Furthermore, lumichrome and riboflavin secreted by soil rhizobia are also known to function as (i) ecological cues for sensing environmental stress, (ii) growth factors for microbes, plants, and humans, (iii) signals for stomatal functioning in land plants, and (iv) protectants/elicitors of plant defense. The fact that exogenous application of ABA to plant roots caused the same effect as lumichrome on leaf stomatal functioning suggests molecular cross-talk in plant response to environmental stimuli.

Increased production of inosine and guanosine by means of metabolic engineering of the purine pathway in Ashbya gossypii

Background

Inosine and guanosine monophosphate nucleotides are convenient sources of the umami flavor, with attributed beneficial health effects that have renewed commercial interest in nucleotide fermentations. Accordingly, several bacterial strains that excrete high levels of inosine and guanosine nucleosides are currently used in the food industry for this purpose.

Results

In the present study, we show that the filamentous fungus Ashbya gossypii, a natural riboflavin overproducer, excretes high amounts of inosine and guanosine nucleosides to the culture medium. Following a rational metabolic engineering approach of the de novo purine nucleotide biosynthetic pathway, we increased the excreted levels of inosine up to 27-fold.

Conclusions

We generated Ashbya gossypii strains with improved production titers of inosine and guanosine. Our results point to Ashbya gossypii as the first eukaryotic microorganism representing a promising candidate, susceptible to further manipulation, for industrial nucleoside fermentation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0234-4) contains supplementary material, which is available to authorized users.

Construction and fed-batch cultivation of Candida famata with enhanced riboflavin production

Riboflavin (vitamin B2) is an essential nutrition component serving as a precursor of coenzymes FMN and FAD that are involved mostly in reactions of oxidative metabolism. Riboflavin is produced in commercial scale and is used in feed and food industries, and in medicine. The yeast Candida famata (Candida flareri) belongs to the group of so called "flavinogenic yeasts" which overproduce riboflavin under iron limitation. Three genes SEF1, RIB1 and RIB7 coding for a putative transcription factor, GTP cyclohydrolase II and riboflavin synthase, respectively were simultaneously overexpressed in the background of a non-reverting riboflavin producing mutant AF-4, obtained earlier in our laboratory using methods of classical selection (Dmytruk et al. (2011), Metabolic Engineering 13, 82-88). Cultivation conditions of the constructed strain were optimized for shake-flasks and bioreactor cultivations. The constructed strain accumulated up to 16.4g/L of riboflavin in optimized medium in a 7L laboratory bioreactor during fed-batch fermentation.

Enhanced riboflavin production by recombinant Bacillus subtilis RF1 through the optimization of agitation speed

Dissolved oxygen is one of the most important bioprocess parameters that could affect cell growth and product formation, and it is easy to control by changing agitation speed. In this work, the effects of agitation speed on the performance of riboflavin production by recombinant Bacillus subtilis RF1 was investigated in fed-batch fermentation. The lower agitation speed (600 rpm) was beneficial for cell growth and riboflavin biosynthesis in the initial phase of fermentation process. While, during the later phase, higher agitation speed (900 rpm) was favor for cell growth and riboflavin biosynthesis. Thus, a two-stage agitation speed control strategy was proposed based on kinetic analysis, in which the agitation speed was controlled at 600 rpm in the first 26 h and then switched to 900 rpm to maintain high μ for cell growth and high q(p) for riboflavin production during the entire fermentation process. However, it was observed that a sharp increase of agitation speed resulted in an adverse effect on cell growth and riboflavin synthesis within a short time. To avoid this phenomenon, a multi-stage agitation speed control strategy was set up based on the two-stage control strategy, the maximum concentration of riboflavin reached 9.4 g l(-1) in 48 h with the yield of 0.051 g g(-1) by applying this strategy, which were 20.5 and 21.4% over the best results controlled by constant agitation speeds.

Identification and functional characterization of the Caenorhabditis elegans riboflavin transporters rft-1 and rft-2

Two potential orthologs of the human riboflavin transporter 3 (hRFVT3) were identified in the C. elegans genome, Y47D7A.16 and Y47D7A.14, which share 33.7 and 30.5% identity, respectively, with hRFVT3. The genes are tandemly arranged, and we assign them the names rft-1 (for Y47D7A.16) and rft-2 (for Y47D7A.14). Functional characterization of the coding sequences in a heterologous expression system demonstrated that both were specific riboflavin transporters, although the rft-1 encoded protein had greater transport activity. A more detailed examination of rft-1 showed its transport of riboflavin to have an acidic pH dependence, saturability (apparent Km = 1.4 ± 0.5 µM), inhibition by riboflavin analogues, and Na(+) independence. The expression of rft-1 mRNA was relatively higher in young larvae than in adults, and mRNA expression dropped in response to RF supplementation. Knocking down the two transporters individually via RNA interference resulted in a severe loss of fertility that was compounded in a double knockdown. Transcriptional fusions constructed with two fluorophores (rft-1::GFP, and rft-2::mCherry) indicated that rft-1 is expressed in the intestine and a small subset of neuronal support cells along the entire length of the animal. Expression of rft-2 is localized mainly to the intestine and pharynx. We also observed a drop in the expression of the two reporters in animals that were maintained in high riboflavin levels. These results report for the first time the identification of two riboflavin transporters in C. elegans and demonstrate their expression and importance to metabolic function in worms. Absence of transporter function renders worms sterile, making them useful in understanding human disease associated with mutations in hRFVT3.

Modulation of guanosine nucleotides biosynthetic pathways enhanced GDP-L-fucose production in recombinant Escherichia coli

Guanosine 5'-triphosphate (GTP) is the key substrate for biosynthesis of guanosine 5'-diphosphate (GDP)-L-fucose. In this study, improvement of GDP-L-fucose production was attempted by manipulating the biosynthetic pathway for guanosine nucleotides in recombinant Escherichia coli-producing GDP-L-fucose. The effects of overexpression of inosine 5'-monophosphate (IMP) dehydrogenase, guanosine 5'-monophosphate (GMP) synthetase (GuaB and GuaA), GMP reductase (GuaC) and guanosine-inosine kinase (Gsk) on GDP-L-fucose production were investigated in a series of fed-batch fermentations. Among the enzymes tested, overexpression of Gsk led to a significant improvement of GDP-L-fucose production. Maximum GDP-L-fucose concentration of 305.5 ± 5.3 mg l(-1) was obtained in the pH-stat fed-batch fermentation of recombinant E. coli-overexpressing Gsk, which corresponds to a 58% enhancement in the GDP-L-fucose production compared with the control strain overexpressing GDP-L-fucose biosynthetic enzymes. Such an enhancement of GDP-L-fucose production could be due to the increase in the intracellular level of GMP.

Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers

Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.

Metabolic engineering and classic selection of the yeast Candida famata (Candida flareri) for construction of strains with enhanced riboflavin production

Currently, the mutant of the flavinogenic yeast Candida famata dep8 isolated by classic mutagenesis and selection is used for industrial riboflavin production. Here we report on construction of a riboflavin overproducing strain of C. famata using a combination of random mutagenesis based on the selection of mutants resistant to different antimetabolites as well as rational approaches of metabolic engineering. The conventional mutagenesis involved consecutive selection for resistance to riboflavin structural analog 7-methyl-8-trifluoromethyl-10-(1'-d-ribityl)isoalloxazine), 8-azaguanine, 6-azauracil, 2-diazo-5-oxo-L-norleucine and guanosine as well as screening for yellow colonies at high pH. The metabolic engineering approaches involved introduction of additional copies of transcription factor SEF1 and IMH3 (coding for IMP dehydrogenase) orthologs from Debaryomyces hansenii, and the homologous genes RIB1 and RIB7, encoding GTP cyclohydrolase II and riboflavin synthetase, the first and the last enzymes of riboflavin biosynthesis pathway, respectively. Overexpression of the aforementioned genes in riboflavin overproducer AF-4 obtained by classical selection resulted in a 4.1-fold increase in riboflavin production in shake-flask experiments. D. hansenii IMH3 and modified ARO4 genes conferring resistance to mycophenolic acid and fluorophenylalanine, respectively, were successfully used as new dominant selection markers for C. famata.

Molecular and structural characterization of GTP-cyclohydrolase II in Eremothecium ashbyi NRRL Y-1363: cDNA cloning, comparative sequence analysis and molecular modeling

GTP-cyclohydrolase II (GCH II) encoded by RIB1 gene catalyzes the first committed step in the riboflavin biosynthetic pathway. We report here the cloning and characterization of the entire RIB1 ORF (EaRIB1) of 942bp by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE-PCR) in Eremothecium ashbyi where it was found to be present as a single-copy gene. EaRIB1 sequence is available at the GenBank Accession Number EF565374. The putative peptide of 313-aa has a high similarity of 60-70% with GCH II sequences from other ascomycete fungi. Gene expression and alignment studies confirmed the functional annotation of this gene. Homology model was developed with Escherichia coli (PDB 2BZ1) as template to identify the catalytic domains and to explore its functional architecture. We report here the first three-dimensional model of any fungal GCH II which due to its absence in humans assumes significance for anti-fungal drug targeting.

Increased riboflavin production from activated bleaching earth by a mutant strain of Ashbya gossypii

The production of riboflavin from vegetable oil was increased using a mutant strain of Ashbya gossypii. This mutant was generated by treating the wild-type strain with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Riboflavin production was 10-fold higher in the mutant compared to the wild-type strain. The specific intracellular catalase activity after 3 d of culture was 6-fold higher in the mutant than in the wild-type strain. For the mutant, riboflavin production in the presence of 40 mM hydrogen peroxide was 16% less than that in the absence of hydrogen peroxide, whereas it was 56% less for the wild-type strain. The isocitrate lyase (ICL) activity of the mutant was 0.26 mU/mg of protein during the active riboflavin production phase, which was 2.6-fold higher than the wild-type strain. These data indicate that the mutant utilizes the carbon flux from the TCA cycle to the glyoxylate cycle more efficiently than the wild-type strain, resulting in enhanced riboflavin production. This novel mutant has the potential to be of use for industrial-scale riboflavin production from waste-activated bleaching earth (ABE), thereby transforming a useless material into a valuable bioproduct.

Isolation of an oxalate-resistant Ashbya gossypii strain and its improved riboflavin production

An oxalate-resistant strain of Ashbya gossypii was naturally isolated from spores grown on an oxalate-containing medium, and its medium was optimized to improve riboflavin production. Riboflavin production by the resistant strain was three-fold higher than that by the wild-type organism when grown in flask cultures. Medium optimization increased the riboflavin production by the resistant strain to 5 g l⁻¹, which was five-fold higher than that obtained by the wild-type strain. The productivity was reproduced in a 3-l bioreactor. During the early growth phase, the specific activity of isocitrate lyase in the oxalate-resistant strain was slightly higher than that in the wild-type strain. Proteomic analysis of the oxalate-resistant strain revealed that the expression of aldose reductase and cobalamin-independent methionine synthase decreased significantly. This is the first report that describes the natural isolation of a riboflavin producer using an antimetabolite-containing medium to enhance the riboflavin production level. This method should also be useful for improving the productivity of other bioproducts since it does not require any mutations or genetic modifications of the microorganism.

Oxidation of rapeseed oil in waste activated bleaching earth and its effect on riboflavin production in culture of Ashbya gossypii

Long-term behavior of rapeseed oil in waste activated bleaching earth (ABE) and the effect of this oil on riboflavin production in the culture of Ashbya gossypii were investigated. Waste ABE with 40% (w/w) rapeseed oil was stored for 80 d, and the extent of oxidation of rapeseed oil was measured by several analytical methods to determine the chemical properties of the oil at different stages of the oil deterioration process:peroxide value, acid value, concentrations of organic acids, acetaldehyde and unsaturated fatty acid, and content of polymerized triglycerides. Peroxide value, acid value, and concentrations of organic acids and acetaldehyde did not affect riboflavin production. However, the content of polymerized triglycerides markedly increased the viscosity of rapeseed oil and was the main reason for the exponential decrease in riboflavin production. A good correlation between the polymerized triglyceride content or viscosity and riboflavin production in the culture of A. gossypii using rapeseed oil as the sole carbon source was found.