Filamentous fungi in microtiter plates—an easy way to optimize itaconic acid production with Aspergillus terreus

High-throughput process development from gene cloning to protein production

In the post-genomic era, the demand for faster and more efficient protein production has increased, both in public laboratories and industry. In addition, with the expansion of protein sequences in databases, the range of possible enzymes of interest for a given application is also increasing. Faced with peer competition, budgetary, and time constraints, companies and laboratories must find ways to develop a robust manufacturing process for recombinant protein production. In this review, we explore high-throughput technologies for recombinant protein expression and present a holistic high-throughput process development strategy that spans from genes to proteins. We discuss the challenges that come with this task, the limitations of previous studies, and future research directions.

Microbial cell factories based on filamentous bacteria, yeasts, and fungi

BACKGROUND

Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved.

RESULTS

As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains.

CONCLUSIONS

In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.

Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus

The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of LaeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity.

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The Itaconic acid biosynthetic gene cluster is regulated by laeA.

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LaeA is required for production of itaconic acid.

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Overexpression of laeA attenuates genes involved in phosphate acquisition.

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Global regulator engineering increases robustness of itaconic acid production.

Synergistic effects on itaconic acid production in engineered Aspergillus niger expressing the two distinct biosynthesis clusters from Aspergillus terreus and Ustilago maydis

BACKGROUND

Itaconic acid (IA) is a versatile platform chemical widely used for the synthesis of various polymers and current methods for IA production based on Aspergillus terreus fermentation are limited in terms of process efficiency and productivity. To construct more efficient IA production strains, A. niger was used as a chassis for engineering IA production by assembling the key components of IA biosynthesis pathways from both A. terreus and Ustilago maydis.

RESULTS

Recombinant A. niger S1596 overexpressing the A. terreus IA biosynthesis genes cadA, mttA, mfsA produced IA of 4.32 g/L, while A. niger S2120 overexpressing the U. maydis IA gene cluster adi1, tad1, mtt1, itp1 achieved IA of 3.02 g/L. Integration of the two IA production pathways led to the construction of A. niger S2083 with IA titers of 5.58 g/L. Increasing cadA copy number in strain S2083 created strain S2209 with titers of 7.99 g/L and deleting ictA to block IA degradation in S2209 created strain S2288 with IA titers of 8.70 g/L. Overexpressing acoA to enhance the supply of IA precursor in strain S2288 generated strain S2444 with IA titers of 9.08 g/L in shake flask.

CONCLUSION

Recombinant A. niger overexpressing the U. maydis IA biosynthesis pathway was capable of IA accumulation. Combined expression of the two IA biosynthesis pathways from A. terreus and U. maydis in A. niger resulted in much higher IA titers. Furthermore, increasing cadA copy number, deleting ictA to block IA degradation and overexpressing acoA to enhance IA precursor supply all showed beneficial effects on IA accumulation.

Evaluation of microtiter plate as a high-throughput screening platform for beer fermentation

Downscaling the anaerobic fermentation in a microtiter plate (MTP) facilitates high throughput screening (HTS) applications. This study investigates the impacts of MTP configurations (scale, shaking, and cover) on the S. pastorianus beer fermentation compared to that in the shaking flask (SF) and European Brewing Convention (EBC) tube regarding fermentation performances and flavor attributes. The lager strains in MTPs accelerated cells reproduction and vitalization, sugar consumption, and glycerol accumulation. The microscale beer fermentation was closer to the SF but differed greatly from EBC tube fermentation depending on the MTP configurations. The downscaling from 2 mL to 0.2 mL in MTP increased the cell growth rate and vitality but did not change the maximum cell density. The shaking MTP did not promote early growth but sustained significantly higher cell numbers at the later fermentation stage. More than 1.5-folds acetaldehyde and higher alcohols, yet less than half esters, were obtained from the MTP and SF fermentations relative to that in the EBC tube. The air-tight MTP cover, as compared to the gas-permeable cover, not only balanced the above volatile flavors but also maintained integrity to the endogenous carbon dioxide pressure during beer fermentation. Additionally, fermentative activities were reduced by excluding air in either the material or the headspace of MTP. Hence, MTP configurations influenced S. pastorianus beer fermentation. These influences were partly attributed to their impacts on air accessibility. Conscious of the impacts, this study helps interpret the minimized fermentation and sheds light on the development of MTP based HTS platform for anaerobic cultivations.

Microbial itaconic acid production from starchy food waste by newly isolated thermotolerant Aspergillus terreus strain

In the present study, we have explored the potential of newly isolated Aspergillus terreus BD strain, which can accumulate itaconic acid (IA) at higher temperature. The shake flask cultivation of thermotolerant strain with medium optimized using Box-Behnken Design at 45 °C resulted in IA accumulation of 28.9 g/L with yield of 0.27 g/g. The enzymatic saccharification of the synthetic food waste (SFW) consisting of potatoes, rice & noodles were optimized using Taguchi method of orthogonal array to maximize the release of fermentable sugar. The maximum glucose release of 0.60 g/g was achieved with 10% biomass loading, 5% enzyme concentration, pH 5.5 and temperature 60 ⁰C. The sugars obtained from SFW was integrated with IA production and maximum IA titer achieved with SFW hydrolysate during bioreactor cultivation was 41.1 g/L with conversion yield of 0.27 g/g while with pure glucose IA titer and yield were 44.7 g/L and 0.30 g/g, respectively.

Something old, something new: challenges and developments in Aspergillus niger biotechnology

The filamentous ascomycete fungus Aspergillus niger is a prolific secretor of organic acids, proteins, enzymes and secondary metabolites. Throughout the last century, biotechnologists have developed A. niger into a multipurpose cell factory with a product portfolio worth billions of dollars each year. Recent technological advances, from genome editing to other molecular and omics tools, promise to revolutionize our understanding of A. niger biology, ultimately to increase efficiency of existing industrial applications or even to make entirely new products. However, various challenges to this biotechnological vision, many several decades old, still limit applications of this fungus. These include an inability to tightly control A. niger growth for optimal productivity, and a lack of high-throughput cultivation conditions for mutant screening. In this mini-review, we summarize the current state-of-the-art for A. niger biotechnology with special focus on organic acids (citric acid, malic acid, gluconic acid and itaconic acid), secreted proteins and secondary metabolites, and discuss how new technological developments can be applied to comprehensively address a variety of old and persistent challenges.

Aspegillus terreus: From Soil to Industry and Back

Aspergillus terreus is an important saprophytic filamentous fungus that can be found in soils. Like many other soil microorganisms, A. terreus demonstrates multiple functions and offers various important metabolites, which can be used in different fields of human activity. The first application of A. terreus on an industrial level is the production of itaconic acid, which is now considered as one of the most important bioproducts in the Green Chemistry field. The general schemes for itaconic acid production have been studied, but in this mini-review some lines of future research are presented based on analysis of the published results. A. terreus is also intensively studied for its biocontrol activity and plant growth-promoting effect. However, this microorganism is also known to infect important crops such as, amongst others, rice, wheat, potato, sugar cane, maize, and soybean. It was suggested, however, that the balance between positive vs. negative effects is dependent on the soil-plant-inoculant dose system. A. terreus has frequently been described as an important human pathogen. Therefore, its safety manipulation in biotechnological processes for the production of itaconic acid and some drugs and its use in soil-plant systems should be carefully assessed. Some suggestions in this direction are discussed, particularly concerning the uses in crop production.

High throughput, small scale methods to characterise the growth of marine fungi

Various marine fungi have been shown to produce interesting, bioactive compounds, but scaling up the production of these compounds can be challenging, particularly because little is generally known about how the producing organisms grow. Here we assessed the suitability of using 100-well BioScreen plates or 96-well plates incubated in a robot hotel to cultivate eight filamentous marine fungi, six sporulating and two non-sporulating, to obtain data on growth and substrate (glucose, xylose, galactose or glycerol) utilisation in a high throughput manner. All eight fungi grew in both cultivation systems, but growth was more variable and with more noise in the data in the Cytomat plate hotel than in the BioScreen. Specific growth rates between 0.01 (no added substrate) and 0.07 h^-1 were measured for strains growing in the BioScreen and between 0.01 and 0.27 h^-1 for strains in the plate hotel. Three strains, Dendryphiella salina LF304, Penicillium chrysogenum KF657 and Penicillium pinophilum LF458, consistently had higher specific growth rates on glucose and xylose in the plate hotel than in the BioScreen, but otherwise results were similar in the two systems. However, because of the noise in data from the plate hotel, the data obtained from it could only be used to distinguish between substrates which did or did not support growth, whereas data from BioScreen also provided information on substrate preference. Glucose was the preferred substrate for all strains, followed by xylose and galactose. Five strains also grew on glycerol. Therefore it was important to minimise the amount of glycerol introduced with the inoculum to avoid misinterpreting the results for growth on poor substrates. We concluded that both systems could provide physiological data with filamentous fungi, provided sufficient replicates are included in the measurements.

Itaconic acid production from undetoxified enzymatic hydrolysate of bamboo residues using Aspergillus terreus

Itaconic acid (IA) production by fermentation of undetoxified hydrolysate of bamboo residues by Aspergillus terreus was demonstrated. Monosaccharides were obtained by pretreatment and enzymatic hydrolysis of bamboo residues. A. terreus could not grow and synthesize IA in the hydrolysate. The buffer was confirmed to be an inhibitor, and was successfully replaced by deionized water as the suspension, to release equivalent sugar and eliminate the inhibition. Corn steep liquor significantly improved the adaptability of A. terreus to the hydrolysate at 2.0 g/L. The IA titer obtained (19.35 g/L IA) was the highest to be reported for IA production from lignocellulose without detoxification. Simultaneous saccharification and fermentation and fed-batch fermentation increased the titer to 22.43 g/L and 41.54 g/L, respectively. Meanwhile, economic assessment proved that bamboo residues were potential substrates for IA production with economic effectiveness.

Biobased Poly(itaconic Acid-co-10-Hydroxyhexylitaconic Acid)s: Synthesis and Thermal Characterization

Renewable vinyl compounds itaconic acid (IA) and its derivative 10-hydroxyhexylitaconic acid (10-HHIA) are naturally produced by fungi from biomass. This provides the opportunity to develop new biobased polyvinyls from IA and 10-HHIA monomers. In this study, we copolymerized these monomers at different ratios through free radical aqueous polymerization with potassium peroxodisulfate as an initiator, resulting in poly(IA-co-10-HHIA)s with different monomer compositions. We characterized the thermal properties of the polymers by thermogravimetric analysis (TGA) and Fourier-transform infrared spectroscopy (FT-IR). The nuclear magnetic resonance analysis and the gel permeation chromatography showed that the polymerization conversion, yield, and the molecular weights (weight-averaged Mw and number-averaged Mn) of the synthesized poly(IA-co-10-HHIA)s decreased with increasing 10-HHIA content. It is suggested that the hydroxyhexyl group of 10-HHIA inhibited the polymerization. The TGA results indicated that the poly(IA-co-10-HHIA)s continuously decomposed as temperature increased. The FT-IR analysis suggested that the formation of the hydrogen bonds between the carboxyl groups of IA and 10-HHIA in the polymer chains was promoted by heating and consequently the polymer dehydration occurred. To the best of our knowledge, this is the first time that biobased polyvinyls were synthesized using naturally occurring IA derivatives.

Optimized Bioproduction of Itaconic and Fumaric Acids Based on Solid-State Fermentation of Lignocellulosic Biomass

The bioproduction of high-value chemicals such as itaconic and fumaric acids (IA and FA, respectively) from renewable resources via solid-state fermentation (SSF) represents an alternative to the current bioprocesses of submerged fermentation using refined sugars. Both acids are excellent platform chemicals with a wide range of applications in different market, such as plastics, coating, or cosmetics. The use of lignocellulosic biomass instead of food resources (starch or grains) in the frame of a sustainable development for IA and FA bioproduction is of prime importance. Filamentous fungi, especially belonging to the Aspergillus genus, have shown a great capacity to produce these organic dicarboxylic acids. This study attempts to develop and optimize the SSF conditions with lignocellulosic biomasses using A. terreus and A. oryzae to produce IA and FA. First, a kinetic study of SSF was performed with non-food resources (wheat bran and corn cobs) and a panel of pH and moisture conditions was studied during fermentation. Next, a new process using an enzymatic cocktail simultaneously with SSF was investigated in order to facilitate the use of the biomass as microbial substrate. Finally, a large-scale fermentation process was developed for SSF using corn cobs with A. oryzae; this specific condition showed the best yield in acid production. The yields achieved were 0.05 mg of IA and 0.16 mg of FA per gram of biomass after 48 h. These values currently represent the highest reported productions for SSF from raw lignocellulosic biomass.

Efficient itaconic acid production by Aspergillus terreus: Overcoming the strong inhibitory effect of manganese

Itaconic acid (IA), a building block platform chemical, is produced industrially by Aspergillus terreus utilizing glucose. Lignocellulosic biomass can serve as a low cost source of sugars for IA production. However, the fungus could not produce IA from dilute acid pretreated and enzymatically saccharified wheat straw hydrolyzate even at 100-fold dilution. Furfural, hydroxymethyl furfural and acetic acid were inhibitory, as is typical, but Mn²⁺ was particularly problematic for IA production. It was present in the hydrolyzate at a level that was 230 times over the inhibitory limit (50 ppb). Recently, it was found that PO₄ ^3- limitation decreased the inhibitory effect of Mn²⁺ on IA production. In the present study, a novel medium was developed for production of IA by varying PO₄ ^3- , Fe³⁺ and Cu²⁺ concentrations using response surface methodology, which alleviated the strong inhibitory effect of Mn²⁺ . The new medium contained 0.08 g KH₂ PO₄ , 3 g NH₄ NO₃ , 1 g MgSO₄ ·7H₂ O, 5 g CaCl₂ ·2 H₂ O, 0.83 mg FeCl₃ ·6H₂ O, 8 mg ZnSO₄ ·7H₂ O, and 45 mg CuSO₄ ·5H₂ O per liter. The fungus was able to produce IA very well in the presence of Mn²⁺ up to 100 ppm in the medium. This medium will be extremely useful for IA production in the presence of Mn²⁺ . This is the first report on the development of Mn²⁺ tolerant medium for IA production by A. terreus.

Metabolic engineering with ATP-citrate lyase and nitrogen source supplementation improves itaconic acid production in Aspergillus niger

BACKGROUND

Bio-based production of organic acids promises to be an attractive alternative for the chemicals industry to substitute petrochemicals as building-block chemicals. In recent years, itaconic acid (IA, methylenesuccinic acid) has been established as a sustainable building-block chemical for the manufacture of various products such as synthetic resins, coatings, and biofuels. The natural IA producer Aspergillus terreus is currently used for industrial IA production; however, the filamentous fungus Aspergillus niger has been suggested to be a more suitable host for this purpose. In our previous report, we communicated the overexpression of a putative cytosolic citrate synthase citB in an A. niger strain carrying the full IA biosynthesis gene cluster from A. terreus, which resulted in the highest final titer reported for A. niger (26.2 g/L IA). In this research, we have attempted to improve this pathway by increasing the cytosolic acetyl-CoA pool. Additionally, we have also performed fermentation optimization by varying the nitrogen source and concentration.

RESULTS

To increase the cytosolic acetyl-CoA pool, we have overexpressed genes acl1 and acl2 that together encode for ATP-citrate lyase (ACL). Metabolic engineering of ACL resulted in improved IA production through an apparent increase in glycolytic flux. Strains that overexpress acl12 show an increased yield, titer and productivity in comparison with parental strain CitB#99. Furthermore, IA fermentation conditions were improved by nitrogen supplementation, which resulted in alkalization of the medium and thereby reducing IA-induced weak-acid stress. In turn, the alkalizing effect of nitrogen supplementation enabled an elongated idiophase and allowed final titers up to 42.7 g/L to be reached at a productivity of 0.18 g/L/h and yield of 0.26 g/g in 10-L bioreactors.

CONCLUSION

Ultimately, this study shows that metabolic engineering of ACL in our rewired IA biosynthesis pathway leads to improved IA production in A. niger due to an increase in glycolytic flux. Furthermore, IA fermentation conditions were improved by nitrogen supplementation that alleviates IA induced weak-acid stress and extends the idiophase.

A closer look at Aspergillus: online monitoring via scattered light enables reproducible phenotyping

BACKGROUND

Filamentously growing microorganisms offer unique advantages for biotechnological processes, such as extraordinary secretion capacities, going along with multiple obstacles due to their complex morphology. However, limited experimental throughput in bioprocess development still hampers taking advantage of their full potential. Miniaturization and automation are powerful tools to accelerate bioprocess development, but so far the application of such technologies has mainly been focused on non-filamentous systems. During cultivation, filamentous fungi can undergo remarkable morphological changes, creating challenging cultivation conditions. Depending on the process and product, only one specific state of morphology may be advantageous to achieve e.g. optimal productivity or yield. Different approaches to control morphology have been investigated, such as microparticle enhanced cultivation. However, the addition of solid microparticles impedes the optical measurements typically used by microbioreactor systems and thus alternatives are needed.

RESULTS

Aspergillus giganteus IfGB 0902 was used as a model system to develop a time-efficient and robust workflow allowing microscale cultivation with increased throughput. The effect of microtiter plate geometry, shaking frequency and medium additives (talc and calcium chloride) on homogeneity of culture morphology as well as reproducibility were analyzed via online biomass measurement, microscopic imaging and cell dry weight. While addition of talc severely affected online measurements, 2% (w v-1) calcium chloride was successfully applied to obtain a highly reproducible growth behavior with homogenous morphology. Furthermore, the influence of small amounts of complex components was investigated for the applied model strain. By correlation to cell dry weight, it could be shown that optical measurements are a suitable signal for biomass concentration. However, each correlation is only applicable for a specific set of cultivation parameters. These optimized conditions were used in micro as well as lab-scale bioreactor cultivation in order to verify the reproducibility and scalability of the setup.

CONCLUSION

A robust workflow for A. giganteus was developed, allowing for reproducible microscale cultivation with online monitoring, where calcium chloride is an useful alternative to microparticle enhanced cultivation in order to control the morphology. Independent of the cultivation volume, comparable phenotypes were observed in microtiter plates and in lab-scale bioreactor.

A high-throughput screening method based on the Mizoroki-Heck reaction for isolating itaconic acid-producing fungi from soils

In this study, we report a novel method based on the Mizoroki-Heck reaction followed by an iodine test for the screening of itaconic acid-producing fungi from soils. This method is simple, rapid, and requires 10 μL of culture; results are obtained within 1.5 h. The detection limit of itaconic acid in the cultures was 0.13 mM. This is the first report on the direct screening of itaconic acid-producing fungi using a coupling reaction.

Malic acid production from biodiesel derived crude glycerol using morphologically controlled Aspergillus niger in batch fermentation

In the present investigation, the effects of crude glycerol concentration, spore inoculum concentration, yeast extract concentration and shaking frequency on seed morphology of Aspergillus niger PJR1 on malic acid production were investigated and dispersed fungal mycelium with higher biomass (20.25 ± 0.91 g/L) was obtained when A. niger PJR1 grow on crude glycerol. Dry cell weight under dispersed fermentation was 21.28% higher than usual pellet fermentation. The optimal crude glycerol, nitrogen source and nitrogen source concentration were found to be 160 g/L, yeast extract and 1.5 g/L, respectively. Batch fermentation in a shake flask culture containing 160 g/L crude glycerol resulted in the yield of malic acid 83.23 ± 1.86 g/L, after 192 h at 25 °C. Results revealed that morphological control of A. niger is an efficient method for increased malic acid production when crude glycerol derived from biodiesel production is used as feedstock.

From beech wood to itaconic acid: case study on biorefinery process integration

Renewable raw materials in sustainable biorefinery processes pose new challenges to the manufacturing routes of platform chemicals. Beside the investigations of individual unit operations, the research on process chains, leading from plant biomass to the final products like lactic acid, succinic acid, and itaconic acid is increasing. This article presents a complete process chain from wooden biomass to the platform chemical itaconic acid. The process starts with the mechanical pretreatment of beech wood, which subsequently is subjected to chemo-catalytic biomass fractionation (OrganoCat) into three phases, which comprise cellulose pulp, aqueous hydrolyzed hemicellulose, and organic lignin solutions. Lignin is transferred to further chemical valorization. The aqueous phase containing oxalic acid as well as hemi-cellulosic sugars is treated by nanofiltration to recycle the acid catalyst back to the chemo-catalytic pretreatment and to concentrate the sugar hydrolysate. In a parallel step, the cellulose pulp is enzymatically hydrolyzed to yield glucose, which-together with the pentose-rich stream-can be used as a carbon source in the fermentation. The fermentation of the sugar fraction into itaconic acid can either be performed with the established fungi Aspergillus terreus or with Ustilago maydis. Both fermentation concepts were realized and evaluated. For purification, (in situ) filtration, (in situ) extraction, and crystallization were investigated. The presented comprehensive examination and discussion of the itaconate synthesis process-as a case study-demonstrates the impact of realistic process conditions on product yield, choice of whole cell catalyst, chemocatalysts and organic solvent system, operation mode, and, finally, the selection of a downstream concept.

Factors Affecting Production of Itaconic Acid from Mixed Sugars by Aspergillus terreus

Itaconic acid (IA; a building block platform chemical) is currently produced industrially from glucose by fermentation with Aspergillus terreus. In order to expand the use of IA, its production cost must be lowered. Lignocellulosic biomass has the potential to serve as low-cost source of sugars for IA production. It was found that the fungus cannot produce IA from dilute acid pretreated and enzymatically saccharified wheat straw hydrolysate even at 100-fold dilution. The effects of typical compounds (acetic acid, furfural, HMF and Mn²⁺, enzymes, CaSO₄), culture conditions (initial pH, temperature, aeration), and medium components (KH₂PO₄, NH₄NO₃, CaCl₂·2H₂O, FeCl₃·6H₂O) on growth and IA production by A. terreus NRRL 1972 using mixed sugar substrate containing glucose, xylose, and arabinose (4:3:1, 80 g L^-1) mimicking the wheat straw hydrolysate were investigated. Acetic acid, furfural, Mn²⁺, and enzymes were strong inhibitors to both growth and IA production from mixed sugars. Optimum culture conditions (pH 3.1, 33 °C, 200 rpm) and medium components (0.8 g KH₂PO₄, 3 g NH₄NO₃, 2.0 g CaCl₂·2H₂O, 0.83-3.33 mg FeCl₃·6H₂O per L) as well as tolerable levels of inhibitors (0.4 g acetic acid, < 0.1 g furfural, 100 mg HMF, < 5.0 ppb Mn²⁺, 24 mg CaSO₄ per L) for mixed sugar utilization were established. The results will be highly useful for developing a bioprocess technology for IA production from lignocellulosic feedstocks.

Enhanced production of l-lactic acid by Lactobacillus thermophilus SRZ50 mutant generated by high-linear energy transfer heavy ion mutagenesis

The aim of this study was to improve l-lactic acid production of Lactobacillus thermophilus SRZ50. For this purpose, high efficient heavy-ion mutagenesis technique was performed using SRZ50 as the original strain. To enhance the screening efficiency for high yield l-lactic acid producers, a scale-down from shake flask to microtiter plate was developed. The results showed that 24-well U-bottom MTPs could well alternate shake flasks for L. thermophilus cultivation as a scale-down tool due to its a very good comparability to the shake flasks. Based on this microtiter plate screening method, two high l-lactic acid productivity mutants, A59 and A69, were successfully screened out, which presented, respectively, 15.8 and 16.2% higher productivities than that of the original strain. Based on fed-batch fermentation, the A69 mutant can accumulate 114.2 g/L l-lactic acid at 96 h. Hence, the proposed traditional microbial breeding method with efficient high-throughput screening assay was proved to be an appropriate strategy to obtain lactic acid-overproducing strain.

A Transcription Factor-Based Biosensor for Detection of Itaconic Acid

Itaconic acid is an important platform chemical that can easily be incorporated into polymers and has the potential to replace petrochemical-based acrylic or methacrylic acid. A number of microorganisms have been developed for the biosynthesis of itaconate including Aspergillus terreus, Escherichia coli, and Saccharomyces cerevisiae. However, the number of strains and conditions that can be tested for increased itaconate titers are currently limited because of the lack of high-throughput screening methods. Here we identified itaconate-inducible promoters and their corresponding LysR-type transcriptional regulators from Yersinia pseudotuberculosis and Pseudomonas aeruginosa. We show that the YpItcR/P ccl inducible system is highly inducible by itaconic acid in the model gammaproteobacterium E. coli and the betaproteobacterium Cupriavidus necator (215- and 105-fold, respectively). The kinetics and dynamics of the YpItcR/P ccl inducible system are investigated, and we demonstrate, that in addition to itaconate, the genetically encoded biosensor is capable of detecting mesaconate, cis-, and trans-aconitate in a dose-dependent manner. Moreover, the fluorescence-based biosensor is applied in E. coli to identify the optimum expression level of cadA, the product of which catalyzes the conversion of cis-aconitate into itaconate. The fluorescence output is shown to correlate well with itaconate concentrations quantified using high-performance liquid chromatography coupled with ultraviolet spectroscopy. This work highlights the potential of the YpItcR/P ccl inducible system to be applied as a biosensor for high-throughput microbial strain development to facilitate improved itaconate biosynthesis.

Microtiter miniature shaken bioreactor system as a scale-down model for process development of production of therapeutic alpha-interferon2b by recombinant Escherichia coli

Background

Demand for high-throughput bioprocessing has dramatically increased especially in the biopharmaceutical industry because the technologies are of vital importance to process optimization and media development. This can be efficiently boosted by using microtiter plate (MTP) cultivation setup embedded into an automated liquid-handling system. The objective of this study was to establish an automated microscale method for upstream and downstream bioprocessing of α-IFN2b production by recombinant Escherichia coli. The extraction performance of α-IFN2b by osmotic shock using two different systems, automated microscale platform and manual extraction in MTP was compared.

Results

The amount of α-IFN2b extracted using automated microscale platform (49.2 μg/L) was comparable to manual osmotic shock method (48.8 μg/L), but the standard deviation was 2 times lower as compared to manual osmotic shock method. Fermentation parameters in MTP involving inoculum size, agitation speed, working volume and induction profiling revealed that the fermentation conditions for the highest production of α-IFN2b (85.5 μg/L) was attained at inoculum size of 8%, working volume of 40% and agitation speed of 1000 rpm with induction at 4 h after the inoculation.

Conclusion

Although the findings at MTP scale did not show perfect scalable results as compared to shake flask culture, but microscale technique development would serve as a convenient and low-cost solution in process optimization for recombinant protein.

Promoters from the itaconate cluster of Ustilago maydis are induced by nitrogen depletion

Background

Ustilago maydis is known for its natural potential to produce a broad range of valuable chemicals, such as itaconate, from both industrial carbon waste streams and renewable biomass. Production of itaconate, and many other secondary metabolites, is induced by nitrogen limitation in U. maydis. The clustered genes responsible for itaconate production have recently been identified, enabling the development of new expression tools that are compatible with biotechnological processes.

Results

Here we report on the investigation of two of the native promoters, P_tad1 and P_mtt1, from the itaconate cluster of U. maydis MB215. For both promoters the specific activation upon nitrogen limitation, which is known to be the trigger for itaconate production in Ustilago, could be demonstrated by gfp expression. The promoters cover a broad range of expression levels, especially when combined with the possibility to create single- and multicopy construct integration events. In addition, these reporter constructs enable a functional characterization of gene induction patterns associated with itaconate production.

Conclusions

The promoters are well suited to induce gene expression in response to nitrogen limitation, coupled to the itaconate production phase, which contributes towards the further improvement of organic acid production with Ustilago.

Production of itaconic acid by biotransformation of wheat bran hydrolysate with Aspergillus terreus CICC40205 mutant

The replacement of the carbon source in the microbial production of itaconic acid (IA) with economic alternatives has attracted significant attention. In this study, an Aspergillus terreus CICC40205 mutant was used to increase the IA titer and decrease the citric acid titer in the wheat bran hydrolysate compared with the parental strain. The results showed that the IA titer was increased by 33.4%, whereas the citric acid titer was decreased by 75.8%, and were in accordance with those of the improved pathway of co-metabolism of glucose and xylose according to the metabolic flux analysis. Additionally, the maximum IA titer obtained in a 7-L stirred tank was 49.65gL^-1±0.38gL^-1. Overall, A. terreus CICC40205 showed a great potential for the industrial production of IA through the biotransformation of the wheat bran hydrolysate.

Microtiter plate-based cultivation to investigate the growth of filamentous fungi

Microscale bioprocessing techniques are rapidly emerging as a means to increase the speed of bioprocess design and to reduce material consumption. However, there is still a lack of suitable parallelized techniques to investigate the industrially important group of filamentous bacteria and fungi. Cultivation of filamentous organisms in shake flasks is still the favored technique for comparing and optimizing cultivation conditions of production strains at mL-scale. In this paper, the application of a microtiter plate-based cultivation system in combination with the filamentous fungus Aspergillus niger was investigated. A protocol for reproducible cultivation was developed and evaluated. Productivity of A. niger concerning the rose-like aroma compound 2-phenylethanol showed low standard deviations while regular and consistent morphologies appeared in the parallelized system. Furthermore, the effect of addition of microparticles on the morphology was investigated. The results can be used to accelerate the process development with A. niger and other filamentous organisms.

Efficient itaconic acid production from glycerol with Ustilago vetiveriae TZ1

BACKGROUND

The family of Ustilaginaceae is known for their capability to naturally produce industrially valuable chemicals from different carbon sources. Recently, several Ustilaginaceae were reported to produce organic acids from glycerol, which is the main side stream in biodiesel production.

RESULTS

In this study, we present Ustilago vetiveriae as new production organism for itaconate synthesis from glycerol. In a screening of 126 Ustilaginaceae, this organism reached one of the highest titers for itaconate combined with a high-glycerol uptake rate. By adaptive laboratory evolution, the production characteristics of this strain could be improved. Further medium optimization with the best single colony, U. vetiveriae TZ1, in 24-deep well plates resulted in a maximal itaconate titer of 34.7 ± 2.5 g L^-1 produced at a rate of 0.09 ± 0.01 g L^-1 h^-1 from 196 g L^-1 glycerol. Simultaneously, this strain produced 46.2 ± 1.4 g L^-1 malate at a rate of 0.12 ± 0.00 g L^-1 h^-1. Due to product inhibition, the itaconate titer in NaOH-titrated bioreactor cultivations was lower (24 g L^-1). Notably, an acidic pH value of 5.5 resulted in decreased itaconate production, however, completely abolishing malate production. Overexpression of ria1 or mtt1, encoding a transcriptional regulator and mitochondrial transporter, respectively, from the itaconate cluster of U. maydis resulted in a 2.0-fold (ria1) and 1.5-fold (mtt1) higher itaconate titer in comparison to the wild-type strain, simultaneously reducing malate production by 75 and 41%, respectively.

CONCLUSIONS

The observed production properties of U. vetiveriae TZ1 make this strain a promising candidate for microbial itaconate production. The outcome of the overexpression experiments, which resulted in reduced malate production in favor of an increased itaconate titer, clearly strengthens its potential for industrial itaconate production from glycerol as major side stream of biodiesel production.

Emerging biotechnologies for production of itaconic acid and its applications as a platform chemical

Recently, itaconic acid (IA), an unsaturated C5-dicarboxylic acid, has attracted much attention as a biobased building block chemical. It is produced industrially (&gt;80 g L−1) from glucose by fermentation with Aspergillus terreus. The titer is low compared with citric acid production (&gt;200 g L−1). This review summarizes the latest progress on enhancing the yield and productivity of IA production. IA biosynthesis involves the decarboxylation of the TCA cycle intermediate cis-aconitate through the action of cis-aconitate decarboxylase (CAD) enzyme encoded by the CadA gene in A. terreus. A number of recombinant microorganisms have been developed in an effort to overproduce it. IA is used as a monomer for production of superabsorbent polymer, resins, plastics, paints, and synthetic fibers. Its applications as a platform chemical are highlighted. It has a strong potential to replace petroleum-based methylacrylic acid in industry which will create a huge market for IA.

Production of lovastatin and itaconic acid by Aspergillus terreus: a comparative perspective

Aspergillus terreus is a textbook example of an industrially relevant filamentous fungus. It is used for the biotechnological production of two valuable metabolites, namely itaconic acid and lovastatin. Itaconic acid serves as a precursor in polymer industry, whereas lovastatin found its place in the pharmaceutical market as a cholesterol-lowering statin drug and a precursor for semisynthetic statins. Interestingly, their biosynthetic gene clusters were shown to reside in the common genetic neighborhood. Despite the genomic proximity of the underlying biosynthetic genes, the production of lovastatin and itaconic acid was shown to be favored by different factors, especially with respect to pH values of the broth. While there are several reviews on various aspects of lovastatin and itaconic acid production, the survey on growth conditions, biochemistry and morphology related to the formation of these two metabolites has never been presented in the comparative manner. The aim of the current review is to outline the correlations and contrasts with respect to process-related and biochemical discoveries regarding itaconic acid and lovastatin production by A. terreus.

Fabrication of multifunctional fluorescent organic nanoparticles with AIE feature through photo-initiated RAFT polymerization

Novel fluorescent organic nanoparticles with AIE feature have been fabricated through a catalyst-free photo-initiated RAFT polymerization.

Rewiring a secondary metabolite pathway towards itaconic acid production in Aspergillus niger

BACKGROUND

The industrially relevant filamentous fungus Aspergillus niger is widely used in industry for its secretion capabilities of enzymes and organic acids. Biotechnologically produced organic acids promise to be an attractive alternative for the chemical industry to replace petrochemicals. Itaconic acid (IA) has been identified as one of the top twelve building block chemicals which have high potential to be produced by biotechnological means. The IA biosynthesis cluster (cadA, mttA and mfsA) has been elucidated in its natural producer Aspergillus terreus and transferred to A. niger to enable IA production. Here we report the rewiring of a secondary metabolite pathway towards further improved IA production through the overexpression of a putative cytosolic citrate synthase citB in a A. niger strain carrying the IA biosynthesis cluster.

RESULTS

We have previously shown that expression of cadA from A. terreus results in itaconic acid production in A. niger AB1.13, albeit at low levels. This low-level production is boosted fivefold by the overexpression of mttA and mfsA in itaconic acid producing AB1.13 CAD background strains. Controlled batch cultivations with AB1.13 CAD + MFS + MTT strains showed increased production of itaconic acid compared with AB1.13 CAD strain. Moreover, preliminary RNA-Seq analysis of an itaconic acid producing AB1.13 CAD strain has led to the identification of the putative cytosolic citrate synthase citB which was induced in an IA producing strain. We have overexpressed citB in a AB1.13 CAD + MFS + MTT strain and by doing so hypothesize to have targeted itaconic acid production to the cytosolic compartment. By overexpressing citB in AB1.13 CAD + MFS + MTT strains in controlled batch cultivations we have achieved highly increased titers of up to 26.2 g/L IA with a productivity of 0.35 g/L/h while no CA was produced.

CONCLUSIONS

Expression of the IA biosynthesis cluster in Aspergillus niger AB1.13 strain enables IA production. Moreover, in the AB1.13 CAD strain IA production resulted in overexpression of a putative cytosolic citrate synthase citB. Upon overexpression of citB we have achieved titers of up to 26.2 g/L IA with a productivity of 0.35 g/L/h in controlled batch cultivations. By overexpressing citB we have also diminished side product formation and optimized the production pathway towards IA.

Enhanced malic acid production from glycerol with high-cell density Ustilago trichophora TZ1 cultivations

BACKGROUND

In order to establish a cost-efficient biodiesel biorefinery, valorization of its main by-product, crude glycerol, is imperative. Recently, Ustilago trichophora TZ1 was found to efficiently produce malic acid from glycerol. By adaptive laboratory evolution and medium optimization, titer and rate could be improved significantly.

RESULTS

Here we report on the investigation of this strain in fed-batch bioreactors. With pH controlled at 6.5 (automatic NaOH addition), a titer of 142 ± 1 g L(-1) produced at an overall rate of 0.54 ± 0.00 g L(-1) h(-1) was reached by optimizing the initial concentrations of ammonium and glycerol. Combining the potential of bioreactors and CaCO3 as buffer system, we were able to increase the overall production rate to 0.74 ± 0.06 g L(-1) h(-1) with a maximum production rate of 1.94 ± 0.32 g L(-1) reaching a titer of 195 ± 15 g L(-1). The initial purification strategy resulted in 90 % pure calcium malate as solid component. Notably, the fermentation is not influenced by an increased temperature of up to 37 °C, which reduces the energy required for cooling. However, direct acid production is not favored as at a lowered pH value of pH 4.5 the malic acid titer decreased to only 9 ± 1 g L(-1). When using crude glycerol as substrate, only the product to substrate yield is decreased. The results are discussed in the context of valorizing glycerol with Ustilaginaceae.

CONCLUSIONS

Combining these results reveals the potential of U. trichophora TZ1 to become an industrially applicable production host for malic acid from biodiesel-derived glycerol, thus making the overall biodiesel production process economically and ecologically more feasible.