Reduced by-product formation and modified oxygen availability improve itaconic acid production in Aspergillus niger

Efficient production of itaconic acid from the single-carbon substrate methanol with engineered Komagataella phaffii

BACKGROUND

Amidst the escalating carbon dioxide levels resulting from fossil fuel consumption, there is a pressing need for sustainable, bio-based alternatives to underpin future global economies. Single-carbon feedstocks, derived from CO2, represent promising substrates for biotechnological applications. Especially, methanol is gaining prominence for bio-production of commodity chemicals.

RESULTS

In this study, we show the potential of Komagataella phaffii as a production platform for itaconic acid using methanol as the carbon source. Successful integration of heterologous genes from Aspergillus terreus (cadA, mttA and mfsA) alongside fine-tuning of the mfsA gene expression, led to promising initial itaconic acid titers of 28 g·L-1 after 5 days of fed-batch cultivation. Through the combined efforts of process optimization and strain engineering strategies, we further boosted the itaconic acid production reaching titers of 55 g·L-1 after less than 5 days of methanol feed, while increasing the product yield on methanol from 0.06 g·g-1 to 0.24 g·g-1.

CONCLUSION

Our results highlight the potential of K. phaffii as a methanol-based platform organism for sustainable biochemical production.

A CRISPR/Cas9-based multicopy integration system for protein production in Aspergillus niger

The filamentous fungus Aspergillus niger is well known for its high protein secretion capacity and a preferred host for homologous and heterologous protein production. To improve the protein production capacity of A. niger even further, a set of dedicated protein production strains was made containing up to 10 glucoamylase landing sites (GLSs) at predetermined sites in the genome. These GLSs replace genes encoding enzymes abundantly present or encoding unwanted functions. Each GLS contains the promotor and terminator region of the glucoamylase gene (glaA), one of the highest expressed genes in A. niger. Integrating multiple gene copies, often realized by random integration, is known to boost protein production yields. In our approach the GLSs allow for rapid targeted gene replacement using CRISPR/Cas9-mediated genome editing. By introducing the same or different unique DNA sequences (dubbed KORE sequences) in each GLS and designing Cas9-compatible single guide RNAs, one is able to select at which GLS integration of a target gene occurs. In this way a set of identical strains with different copy numbers of the gene of interest can be easily and rapidly made to compare protein production levels. As an illustration of its potential, we successfully used the expression platform to generate multicopy A. niger strains producing the Penicillium expansum PatE::6xHis protein catalysing the final step in patulin biosynthesis. The A. niger strain expressing 10 copies of the patE::6xHis expression cassette produced about 70 μg·mL-1 PatE protein in the culture medium with a purity just under 90%.

Effect of different metabolic pathways on itaconic acid production in engineered Corynebacterium glutamicum

Itaconic acid (IA), a C5-dicarboxylic acid, is a potential bio-based building block for the polymer industry. There are three pathways for IA production from natural IA producers; however, most of the engineered strains were used for IA production by heterologous expression of cis-aconitate decarboxylase gene (cadA) from Aspergillus terreus. In this study, IA was produced by an engineered Corynebacterium glutamicum ATCC 13032 expressing two different types of genes from two distinct pathways. The first involves the mammalian immunoresponsive gene1 (Irg1) derived from Mus musculus. The second (termed here the trans-pathway) involves two genes from the natural IA producer Ustilago maydis which are aconitate-delta-isomerase (Adi1) and trans-aconitate decarboxylase (Tad1) genes. The constructed strains developing the two distinct IA production pathways: C. glutamicum ATCC 13032 pCH-Irg1_opt and C. glutamicum ATCC 13032 pCH-Tad1_optadi1_opt were used for production of IA from different carbon sources. The results reflect the possibility for IA production from C. glutamicum expressing the trans-pathway (Adi1/Tad1 genes) and cis-pathway (Irg1 gene) other than the well-known cis-pathway that depends mainly on cadA gene from A. terreus. The developed strain expressing trans-pathway from U. maydis; however, proved to be better at IA production with high titers of 12.25, 11.34, and 11.02 g/L, and a molar yield of 0.22, 0.42, and 0.43 mol/mol from glucose, maltose, and sucrose, respectively, via fed-batch fermentation. The present study suggests that trans-pathway is better than cis-pathway for IA production in engineered C. glutamicum.

Recent Advances on the Production of Itaconic Acid via the Fermentation and Metabolic Engineering

Itaconic acid (ITA) is one of the top 12 platform chemicals. The global ITA market is expanding due to the rising demand for bio-based unsaturated polyester resin and its non-toxic qualities. Although bioconversion using microbes is the main approach in the current industrial production of ITA, ecological production of bio-based ITA faces several issues due to: low production efficiency, the difficulty to employ inexpensive raw materials, and high manufacturing costs. As metabolic engineering advances, the engineering of microorganisms offers a novel strategy for the promotion of ITA bio-production. In this review, the most recent developments in the production of ITA through fermentation and metabolic engineering are compiled from a variety of perspectives, including the identification of the ITA synthesis pathway, the metabolic engineering of natural ITA producers, the design and construction of the ITA synthesis pathway in model chassis, and the creation, as well as application, of new metabolic engineering strategies in ITA production. The challenges encountered in the bio-production of ITA in microbial cell factories are discussed, and some suggestions for future study are also proposed, which it is hoped offers insightful views to promote the cost-efficient and sustainable industrial production of ITA.

The Influence of Hydrodynamic Conditions in a Laboratory-Scale Bioreactor on Pseudomonas aeruginosa Metabolite Production

Hydrodynamic conditions are critical in bioprocessing because they influence oxygen availability for cultured cells. Processes in typical laboratory bioreactors need optimization of these conditions using mixing and aeration control to obtain high production of the desired bioproduct. It could be done by experiments supported by computational fluid dynamics (CFD) modeling. In this work, we characterized parameters such as mixing time, power consumption and mass transfer in a 2 L bioreactor. Based on the obtained results, we chose a set of nine process parameters to test the hydrodynamic impact on a selected bioprocess (mixing in the range of 0-160 rpm and aeration in the range of 0-250 ccm). Therefore, we conducted experiments with P. aeruginosa culture and assessed how various hydrodynamic conditions influenced biomass, pyocyanin and rhamnolipid production. We found that a relatively high mass transfer of oxygen (k_La = 0.0013 s^-1) connected with intensive mixing (160 rpm) leads to the highest output of pyocyanin production. In contrast, rhamnolipid production reached maximal efficiency under moderate oxygen mass transfer (k_La = 0.0005 s^-1) and less intense mixing (in the range of 0-60 rpm). The results indicate that manipulating hydrodynamics inside the bioreactor allows control of the process and may lead to a change in the metabolites produced by bacterial cells.

Conversion of CO2 into organic acids by engineered autotrophic yeast

The increase of CO2 emissions due to human activity is one of the preeminent reasons for the present climate crisis. In addition, considering the increasing demand for renewable resources, the upcycling of CO2 as a feedstock gains an extensive importance to establish CO2-neutral or CO2-negative industrial processes independent of agricultural resources. Here we assess whether synthetic autotrophic Komagataella phaffii (Pichia pastoris) can be used as a platform for value-added chemicals using CO2 as a feedstock by integrating the heterologous genes for lactic and itaconic acid synthesis. 13C labeling experiments proved that the resulting strains are able to produce organic acids via the assimilation of CO2 as a sole carbon source. Further engineering attempts to prevent the lactic acid consumption increased the titers to 600 mg L-1, while balancing the expression of key genes and modifying screening conditions led to 2 g L-1 itaconic acid. Bioreactor cultivations suggest that a fine-tuning on CO2 uptake and oxygen demand of the cells is essential to reach a higher productivity. We believe that through further metabolic and process engineering, the resulting engineered strain can become a promising host for the production of value-added bulk chemicals by microbial assimilation of CO2, to support sustainability of industrial bioprocesses.

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.

John PC, Kumar N. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling

Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.

Biotechnological valorization of cashew apple juice for the production of citric acid by a local strain of Aspergillus niger LCFS 5

Background

This work investigates the production of citric acid from cashew apple juice, an abundant waste in the processing of cashew, using a local strain of Aspergillus niger and the application of the citric acid as a coagulant for the production of soy cheese. Fungal isolates were obtained from a cashew plantation in Ogbomoso, Nigeria, using potato dextrose agar. Further screening was undertaken to determine the qualitative strength of acid production by the fungi on Czapek-Dox agar supplemented with bromocresol green, with the development of yellow zone taken as an indication of citric acid production. Thereafter, the best producing strain was cultivated in a cashew apple juice medium.

Results

Out of 150 fungal isolates generated from the cashew plantation, 92 (61.3%), 44 (29.3%) and 14 (9.3%) were obtained from cashew fruits, soil and cashew tree surfaces, respectively. Different strains of fungi isolated include Aspergillus niger, A. flavus, A. foetidus, A. heteromorphus, A. nidulans and A. viridinutans. The isolates produced yellow zonation of 0.4–5.5 cm on modified Czapek-Dox agar; the highest was observed for a strain of A. niger LCFS 5, which was identified using molecular tools. In the formulated cashew apple juice medium, the citric acid yield of LCFS 5 ranged 16.0–92.8 g/l with the peak obtained on the 10th day of fermentation. The citric acid produced was recovered using the double precipitation method with Ca(OH)₂ and H₂SO₄ having ≈ 70% purity of citric acid on HPLC. The citric acid acted as a coagulant to produce soy cheese with 66.67% acceptability by panelists.

Conclusion

This work has extended the frontiers of valorization of cashew waste by a strain of A. niger to produce citric acid in high yield, with potential application in food industries.

Membrane transporters in the bioproduction of organic acids: state of the art and future perspectives for industrial applications

Organic acids such as monocarboxylic acids, dicarboxylic acids or even more complex molecules such as sugar acids, have displayed great applicability in the industry as these compounds are used as platform chemicals for polymer, food, agricultural and pharmaceutical sectors. Chemical synthesis of these compounds from petroleum derivatives is currently their major source of production. However, increasing environmental concerns have prompted the production of organic acids by microorganisms. The current trend is the exploitation of industrial biowastes to sustain microbial cell growth and valorize biomass conversion into organic acids. One of the major bottlenecks for the efficient and cost-effective bioproduction is the export of organic acids through the microbial plasma membrane. Membrane transporter proteins are crucial elements for the optimization of substrate import and final product export. Several transporters have been expressed in organic acid-producing species, resulting in increased final product titers in the extracellular medium and higher productivity levels. In this review, the state of the art of plasma membrane transport of organic acids is presented, along with the implications for industrial biotechnology.

Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites

Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.

Investigation of Itaconic Acid Separation by Operating a Commercialized Electrodialysis Unit with Bipolar Membranes

Nowadays, the merging of membrane and fermentation technologies is receiving significant attention such as in the case of itaconic acid (IA) production, which is considered as a value-added chemical. Its biotechnological production is already industrially established; however, the improvements of its fermentative and recovery steps remain topics of significant interest due to sustainable development trends. With an adequate downstream process, the total price of IA production can be reduced. For the task of IA recovery, a contemporary electro-membrane separation processes, electrodialysis with bipolar membranes (EDBM), was proposed and employed in this work. In the experiments, the laboratory-scale, commercialized EDBM unit (P EDR-Z/4x) was operated to separate IA from various model solutions compromised of IA (5–33 g/L), glucose (varied in 15–33 g/L as a residual substrate during IA fermentation) and malic acid (varied in 0–1 g/L as a realistic by-product of IA fermentation) under different initial pH (2–5) and applied potential conditions (10–30 V). Unambiguously negative effects related to the glucose and malic acid as impurities were found neither on the IA recovery ratio nor on the current efficiency, falling into the ranges of 90–97% and 74.3–98.5%, respectively. The highest IA recovery ratios of 97% and 98.5% of current efficiency were obtained with the model fermentation solution containing 33 g/L IA, 33 g/L glucose at 20 V and an initial pH of 5. However, the selective separation of IA needs further investigations with a real fermentation broth, and the findings of this research may contribute to further studies in this field.

Production of Itaconic Acid from Cellulose Pulp: Feedstock Feasibility and Process Strategies for an Efficient Microbial Performance

This study assessed the feasibility of using bleached cellulose pulp from Eucalyptus wood as a feedstock for the production of itaconic acid by fermentation. Additionally, different process strategies were tested with the aim of selecting suitable conditions for an efficient production of itaconic acid by the fungus Aspergillus terreus. The feasibility of using cellulose pulp was demonstrated through assays that revealed the preference of the strain in using glucose as carbon source instead of xylose, mannose, sucrose or glycerol. Additionally, the cellulose pulp was easily digested by enzymes without requiring a previous step of pretreatment, producing a glucose-rich hydrolysate with a very low level of inhibitor compounds, suitable for use as a fermentation medium. Fermentation assays revealed that the technique used for sterilization of the hydrolysate (membrane filtration or autoclaving) had an important effect in its composition, especially on the nitrogen content, consequently affecting the fermentation performance. The carbon-to-nitrogen ratio (C:N ratio), initial glucose concentration and oxygen availability, were also important variables affecting the performance of the strain to produce itaconic acid from cellulose pulp hydrolysate. By selecting appropriate process conditions (sterilization by membrane filtration, medium supplementation with 3 g/L (NH4)2SO4, 60 g/L of initial glucose concentration, and oxygen availability of 7.33 (volume of air/volume of medium)), the production of itaconic acid was maximized resulting in a yield of 0.62 g/g glucose consumed, and productivity of 0.52 g/L·h.

Metabolic engineering of an industrial Aspergillus niger strain for itaconic acid production

Itaconic acid is a value-added organic acid that is widely applied in industrial production. It can be converted from citric acid by some microorganisms including Aspergillus terreus and Aspergillus niger. Because of high citric acid production (more than 200 g/L), A. niger strains may be developed into powerful itaconic acid-producing microbial cell factories. In this study, industrial citric acid-producing strain A. niger YX-1217, capable of producing 180.0-200.0 g/L, was modified to produce itaconic acid by metabolic engineering. A key gene cadA encoding aconitase was expressed in A. niger YX-1217 under the control of three different promoters. Analyses showed that the PglaA promoter resulted in higher levels of gene expression than the PpkiA and PgpdA promoters. Moreover, the synthesis pathway of itaconic acid was extended by introducing the acoA gene, and the cadA gene, encoding aconitate decarboxylase, into A. niger YX-1217 under the function of the two rigid short-peptide linkers L₁ or L₂. The resulting recombinant strains L-1 and L-2 were induced to produce itaconic acid in fed-batch fermentations under three-stage control of agitation speed. After fermentation for 104 h, itaconic acid concentrations in the recombinant strain L-2 culture reached 7.2 g/L, which represented a 71.4% increase in itaconic acid concentration compared with strain Z-17 that only expresses cadA. Therefore, co-expression of acoA and cadA resulted in an extension of the citric acid metabolic pathway to the itaconic acid metabolic pathway, thereby increasing the production of itaconic acid by A. niger.

Identification of novel citramalate biosynthesis pathways in Aspergillus niger

Background

The filamentous fungus Aspergillus niger is frequently used for industrial production of fermentative products such as enzymes, proteins and biochemicals. Notable examples of industrially produced A. niger fermentation products are glucoamylase and citric acid. Most notably, the industrial production of citric acid achieves high titers, yield and productivities, a feat that has prompted researchers to propose A. niger to serve as heterologous production host for the industrial production of itaconic acid (IA), a promising sustainable chemical building-block for the fabrication of various synthetic resins, coatings, and polymers. Heterologous production of IA in A. niger has resulted in unexpected levels of metabolic rewiring that has led us to the identification of IA biodegradation pathway in A. niger. In this study we have attempted to identify the final product of the IA biodegradation pathway and analyzed the effect of metabolic rewiring on the bioproduction of 9 industrially relevant organic acids.

Results

IA biodegradation manifests in diminishing titers of IA and the occurrence of an unidentified compound in the HPLC profile. Based on published results on the IA biodegradation pathway, we hypothesized that the final product of IA biodegradation in A. niger may be citramalic acid (CM). Based on detailed HPLC analysis, we concluded that the unidentified compound is indeed CM. Furthermore, by transcriptome analysis we explored the effect of metabolic rewiring on the production of 9 industrially relevant organic acids by transcriptome analysis of IA producing and WT A. niger strains. Interestingly, this analysis led to the identification of a previously unknown biosynthetic cluster that is proposed to be involved in the biosynthesis of CM. Upon overexpression of the putative citramalate synthase and a genomically clustered organic acid transporter, we have observed CM bioproduction by A. niger.

Conclusion

In this study, we have shown that the end product of IA biodegradation pathway in A. niger is CM. Knock-out of the IA biodegradation pathway results in the cessation of CM production. Furthermore, in this study we have identified a citramalate biosynthesis pathway, which upon overexpression drives citramalate bioproduction in A. niger.

Metabolic specialization in itaconic acid production: a tale of two fungi

Some of the oldest and most established industrial biotechnology processes involve the fungal production of organic acids. In these fungi, the transport of metabolites between cellular compartments, and their secretion, is a major factor. In this review we exemplify the importance of both mitochondrial and plasma membrane transporters in the case of itaconic acid production in two very different fungal systems, Aspergillus and Ustilago. Homologous and heterologous overexpression of both types of transporters, and biochemical analysis of mitochondrial transporter function, show that these two fungi produce the same compound through very different pathways. The way these fungi respond to itaconate stress, especially at low pH, also differs, although this is still an open field which clearly needs additional research.

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.

Cell Factory Engineering

Rational approaches to modifying cells to make molecules of interest are of substantial economic and scientific interest. Most of these efforts aim at the production of native metabolites, expression of heterologous biosynthetic pathways, or protein expression. Reviews of these topics have largely focused on individual strategies or cell types, but collectively they fall under the broad umbrella of a growing field known as cell factory engineering. Here we condense >130 reviews and key studies in the art into a meta-review of cell factory engineering. We identified 33 generic strategies in the field, all applicable to multiple types of cells and products, and proven successful in multiple major cell types. These apply to three major categories: production of native metabolites and/or bioactives, heterologous expression of biosynthetic pathways, and protein expression. This meta-review provides general strategy guides for the broad range of applications of rational engineering of cell factories.

Biomass-Derived Production of Itaconic Acid as a Building Block in Specialty Polymers

Biomass, the only source of renewable organic carbon on Earth, offers an efficient substrate for bio-based organic acid production as an alternative to the leading petrochemical industry based on non-renewable resources. Itaconic acid (IA) is one of the most important organic acids that can be obtained from lignocellulose biomass. IA, a 5-C dicarboxylic acid, is a promising platform chemical with extensive applications; therefore, it is included in the top 12 building block chemicals by the US Department of Energy. Biotechnologically, IA production can take place through fermentation with fungi like Aspergillus terreus and Ustilago maydis strains or with metabolically engineered bacteria like Escherichia coli and Corynebacterium glutamicum. Bio-based IA represents a feasible substitute for petrochemically produced acrylic acid, paints, varnishes, biodegradable polymers, and other different organic compounds. IA and its derivatives, due to their trifunctional structure, support the synthesis of a wide range of innovative polymers through crosslinking, with applications in special hydrogels for water decontamination, targeted drug delivery (especially in cancer treatment), smart nanohydrogels in food applications, coatings, and elastomers. The present review summarizes the latest research regarding major IA production pathways, metabolic engineering procedures, and the synthesis and applications of novel polymeric materials.

Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways

BACKGROUND

Itaconic acid (IA), a C5-dicarboxylic acid, has previously been identified as one of the top twelve biochemicals that can be produced by biotechnological means. IA is naturally produced by Aspergillus terreus, however, heterologous production in the related species Aspergillus niger has been proposed earlier. Remarkably, we observed that during high producing conditions and elevated titers A. niger detoxifies the extracellular medium of IA. In order to determine the genes responsible for this decline in IA titers a transcriptome analysis was performed.

RESULTS

Transcriptome analysis has led to the identification of two novel and previously unknown IA bioconversion pathways in A. niger. One pathway is proposed to convert IA into pyruvate and acetyl-CoA through the action of itaconyl-CoA transferase (IctA), itaconyl-CoA hydratase (IchA) and citramalyl-CoA lyase, similar to the pathway identified in A. terreus. Another pathway putatively converts IA into 1-methyl itaconate through the action of trans-aconitate methyltransferase (TmtA). Upon deleting the key genes ictA and ichA we have observed increased IA production and titers and cessation of IA bioconversion. Surprisingly, deletion of tmtA lead to strong reduction of heterologous IA production.

CONCLUSION

Heterologous IA production in A. niger induces the expression of IA bioconversion pathways. These pathways can be inhibited by deleting the key genes ictA, ichA and tmtA. Deletion of ictA and ichA resulted in increased IA production. Deletion of tmtA, however, resulted in almost complete cessation of IA production.

High oxygen tension increases itaconic acid accumulation, glucose consumption, and the expression and activity of alternative oxidase in Aspergillus terreus

Itaconic acid is a five-carbon dicarboxylic acid with an unsaturated alkene bond, frequently used as a building block for the industrial production of a variety of synthetic polymers. It is also one of the major products of fungal "overflow metabolism" which can be produced in submerged fermentations of the filamentous fungus Aspergillus terreus. At the present, molar yields of itaconate are lower than those obtained in citric acid production in Aspergillus niger. Here, we have studied the possibility that the yield may be limited by the oxygen supply during fermentation and hence tested the effect of the dissolved oxygen concentration on the itaconic acid formation rate and yield in lab-scale bioreactors. The data show that a dissolved oxygen concentration of 2% saturation was sufficient for maximal biomass formation. Raising it to 30% saturation had no effect on biomass formation or the growth rate, but the itaconate yield augmented substantially from 0.53 to 0.85 mol itaconate/mol glucose. Furthermore, the volumetric and specific rates of itaconic acid formation ameliorated by as much as 150% concurrent with faster glucose consumption, shortening the fermentation time by 48 h. Further increasing the dissolved oxygen concentration over 30% saturation had no effect. Moreover, we show that this increase in itaconic acid production coincides with an increase in alternative respiration, circumventing the formation of surplus ATP by the cytochrome electron transport chain, as well as with increased levels of alternative oxidase transcript. We conclude that high(er) itaconic acid accumulation requires a dissolved oxygen concentration that is much higher than that needed for maximal biomass formation, and postulate that the induction of alternative respiration allows the necessary NADH reoxidation ratio without surplus ATP production to increase the glucose consumption and the flux through overflow metabolism.

World market and biotechnological production of itaconic acid

The itaconic acid (IA) world market is expected to exceed 216 million of dollars by 2020 as a result of an increasing demand for bio-based chemicals. The potential of this organic acid produced by fermentation mainly with filamentous fungi relies on the vast industrial applications of polymers derived from it. The applications may be as a superabsorbent polymer for personal care or agriculture, unsaturated polyester resin for the transportation industry, poly(methyl methacrylate) for electronic devices, among many others. However, the existence of other substitutes and the high production cost limit the current IA market. IA manufacturing is done mainly in China and other Asia-Pacific countries. Higher economic feasibility and production worldwide may be achieved with the use of low-cost feedstock of local origin and with the development of applications targeted to specific local markets. Moreover, research on the biological pathway for IA synthesis and the effect of medium composition are important for amplifying the knowledge about the production of that biochemical with great market potential.

Soybean hull induced production of carbohydrases and protease among Aspergillus and their effectiveness in soy flour carbohydrate and protein separation

Soybean hull consists mainly of three major plant carbohydrates, i.e., cellulose, hemicellulose and pectin. It is inexpensive and a good potential substrate for carbohydrase production because it is capable of inducing a complete spectrum of activities to hydrolyze complex biomass. Aspergillus is known for carbohydrase production but no studies have evaluated and compared, among Aspergillus species and strains, the soybean hull induced production of various carbohydrases. In this study, A. aculeatus, A. cinnamomeus, A. foetidus, A. phoenicis and 11 A. niger strains were examined together with T. reesei Rut C30, another known carbohydrase producer. The carbohydrases evaluated included pectinase, polygalacturonase, xylanase, cellulase, α-galactosidase and sucrase. Growth morphology and pH profiles were also followed. Among Aspergillus strains, morphology was found to correlate with both carbohydrase production and pH decrease profile. Filamentous strains gave higher carbohydrase production while causing slower pH decrease. The enzyme broths produced were also tested for separation of soy flour carbohydrate and protein. Defatted soy flour contains about 53% protein and 32% carbohydrate. The enzymatic treatment can increase protein content and remove indigestible oligo-/poly-saccharides, and improve use of soy flour in feed and food. Protease production by different strains was therefore also compared for minimizing protein degradation. A. niger NRRL 322 and A. foetidus NRRL 341 were found to be the most potent strains that produced maximal carbohydrases and minimal protease under soybean hull induction.

Pgas, a Low-pH-Induced Promoter, as a Tool for Dynamic Control of Gene Expression for Metabolic Engineering of Aspergillus niger

The dynamic control of gene expression is important for adjusting fluxes in order to obtain desired products and achieve appropriate cell growth, particularly when the synthesis of a desired product drains metabolites required for cell growth. For dynamic gene expression, a promoter responsive to a particular environmental stressor is vital. Here, we report a low-pH-inducible promoter, Pgas, which promotes minimal gene expression at pH values above 5.0 but functions efficiently at low pHs, such as pH 2.0. First, we performed a transcriptional analysis of Aspergillus niger, an excellent platform for the production of organic acids, and we found that the promoter Pgas may act efficiently at low pH. Then, a gene for synthetic green fluorescent protein (sGFP) was successfully expressed by Pgas at pH 2.0, verifying the results of the transcriptional analysis. Next, Pgas was used to express the cis-aconitate decarboxylase (cad) gene of Aspergillus terreus in A. niger, allowing the production of itaconic acid at a titer of 4.92 g/liter. Finally, we found that Pgas strength was independent of acid type and acid ion concentration, showing dependence on pH only.IMPORTANCE The promoter Pgas can be used for the dynamic control of gene expression in A. niger for metabolic engineering to produce organic acids. This promoter may also be a candidate tool for genetic engineering.

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 (>80 g L−1) from glucose by fermentation with Aspergillus terreus. The titer is low compared with citric acid production (>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 itaconate by whole-cell bioconversion of citrate mediated by expression of multiple cis-aconitate decarboxylase (cadA) genes in Escherichia coli

Itaconate, a C₅ unsaturated dicarboxylic acid, is an important chemical building block that is used in manufacturing high-value products, such as latex and superabsorbent polymers. Itaconate is produced by fermentation of sugars by the filamentous fungus Aspergillus terreus. However, fermentation by A. terreus involves a long fermentation period and the formation of various byproducts, resulting in high production costs. E. coli has been developed as an alternative for producing itaconate. However, fermentation of glucose gives low conversion yields and low productivity. Here, we report the whole-cell bioconversion of citrate to itaconate with enhanced aconitase and cis-aconitate decarboxylase activities by controlling the expression of multiple cadA genes. In addition, this bioconversion system does not require the use of buffers, which reduces the production cost and the byproducts released during purification. Using this whole-cell bioconversion system, we were able to catalyze the conversion of 319.8 mM of itaconate (41.6 g/L) from 500 mM citrate without any buffer system or additional cofactors, with 64.0% conversion in 19 h and a productivity of 2.19 g/L/h. Our bioconversion system suggests very high productivity for itaconate production.

Crossing boundaries: the importance of cellular membranes in industrial biotechnology

How small molecules cross cellular membranes is an often overlooked issue in an industrial microbiology and biotechnology context. This is to a large extent governed by the technical difficulties to study these transport systems or by the lack of knowledge on suitable efflux pumps. This review emphasizes the importance of microbial cellular membranes in industrial biotechnology by highlighting successful strategies of membrane engineering towards more resistant and hence better performing microorganisms, as well as transporter and other engineering strategies for increased efflux of primary and secondary metabolites. Furthermore, the benefits and limitations of eukaryotic subcellular compartmentalization are discussed, as well as the biotechnological potential of membrane vesicles.

Waste biorefineries using filamentous ascomycetes fungi: Present status and future prospects

Filamentous ascomycetes fungi have had important roles in natural cycles, and are already used industrially for e.g. supplying of citric, gluconic and itaconic acids as well as many enzymes. Faster human activities result in higher consumption of our resources and producing more wastes. Therefore, these fungi can be explored to use their capabilities to convert back wastes to resources. The present paper reviews the capabilities of these fungi in growing on various residuals, producing lignocellulose-degrading enzymes and production of organic acids, ethanol, pigments, etc. Particular attention has been on Aspergillus, Fusarium, Neurospora and Monascus genera. Since various species are used for production of human food, their biomass can be considered for feed applications and so biomass compositional characteristics as well as aspects related to culture in bioreactor are also provided. The review has been further complemented with future research avenues.

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.

Identification of a Classical Mutant in the Industrial Host Aspergillus niger by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites

The asexual filamentous fungus Aspergillus niger is an important industrial cell factory for citric acid production. In this study, we genetically characterized a UV-generated A. niger mutant that was originally isolated as a nonacidifying mutant, which is a desirable trait for industrial enzyme production. Physiological analysis showed that this mutant did not secrete large amounts of citric acid and oxalic acid, thus explaining the nonacidifying phenotype. As traditional complementation approaches to characterize the mutant genotype were unsuccessful, we used bulk segregant analysis in combination with high-throughput genome sequencing to identify the mutation responsible for the nonacidifying phenotype. Since A. niger has no sexual cycle, parasexual genetics was used to generate haploid segregants derived from diploids by loss of whole chromosomes. We found that the nonacidifying phenotype was caused by a point mutation in the laeA gene. LaeA encodes a putative methyltransferase-domain protein, which we show here to be required for citric acid production in an A. niger lab strain (N402) and in other citric acid production strains. The unexpected link between LaeA and citric acid production could provide new insights into the transcriptional control mechanisms related to citric acid production in A. niger. Interestingly, the secondary metabolite profile of a ΔlaeA strain differed from the wild-type strain, showing both decreased and increased metabolite levels, indicating that LaeA is also involved in regulating the production of secondary metabolites. Finally, we show that our systems genetics approach is a powerful tool to identify trait mutations.

Heterologous expression of Mus musculus immunoresponsive gene 1 (irg1) in Escherichia coli results in itaconate production

Itaconic acid, a C5-dicarboxylic acid, is a potential biobased building block for the polymer industry. It is obtained from the citric acid cycle by decarboxylation of cis-aconitic acid. This reaction is catalyzed by CadA in the native itaconic acid producer Aspergillus terreus. Recently, another enzyme encoded by the mammalian immunoresponsive gene 1 (irg1), was found to decarboxylate cis-aconitate to itaconate in vitro. We show that heterologous expression of irg1 enabled itaconate production in Escherichia coli with production titres up to 560 mg/L.

Pathway transfer in fungi

Itaconic acid is an important building block for the chemical industry. Currently, Aspergillus terreus is the main organism used for itaconic acid production. Due to the enormous citric acid production capacity of Aspergillus niger, this host is investigated as a potential itaconic acid production host. Several strategies have been tried so far: fermentation optimization, expression of cis-aconitate decarboxylase (cadA) alone and in combination with aconitase targeted to the same compartment, chassis optimization, and the heterologous expression of two transporters flanking the cadA gene. We showed that the heterologous expression of these two transporters were key to improving itaconic acid production in an A. niger strain that was unable to produce oxalic acid and gluconic acid. The expression of transporters has increased the production levels of other industrially relevant processes as well, such as β-lactam antibiotics and bioethanol. Thus far, the role of transporters in production process optimization is a bit overlooked.

Mitochondrial engineering of the TCA cycle for fumarate production

Microbial fumarate production from renewable feedstock is a promising and sustainable alternative to petroleum-based chemical synthesis. Here, mitochondrial engineering was used to construct the oxidative pathway for fumarate production starting from the TCA cycle intermediate α-ketoglutarate in Candida glabrata. Accordingly, α-ketoglutarate dehydrogenase complex (KGD), succinyl-CoA synthetase (SUCLG), and succinate dehydrogenase (SDH) were selected to be manipulated for strengthening the oxidative pathway, and the engineered strain T.G-K-S-S exhibited increased fumarate biosynthesis (1.81 g L(-1)). To further improve fumarate production, the oxidative route was optimized. First, three fusion proteins KGD2-SUCLG2, SUCLG2-SDH1 and KGD2-SDH1 were constructed, and KGD2-SUCLG2 led to improved fumarate production (4.24 g L(-1)). In addition, various strengths of KGD2-SUCLG2 and SDH1 expression cassettes were designed by combinations of promoter strengths and copy numbers, resulting in a large increase in fumarate production (from 4.24 g L(-1) to 8.24 g L(-1)). Then, through determining intracellular amino acids and its related gene expression levels, argininosuccinate lyase in the urea cycle was identified as the key factor for restricting higher fumarate production. Correspondingly, after overexpression of it, the fumarate production was further increased to 9.96 g L(-1). Next, two dicarboxylic acids transporters facilitated an improvement of fumarate production, and, as a result, the final strain T.G-KS(H)-S(M)-A-2S reached fumarate titer of 15.76 g L(-1). This strategy described here paves the way to the development of an efficient pathway for microbial production of fumarate.

Direct production of itaconic acid from liquefied corn starch by genetically engineered Aspergillus terreus

Background

Itaconic acid is on the DOE (Department of Energy) top 12 list of biotechnologically produced building block chemicals and is produced commercially by Aspergillus terreus. However, the production cost of itaconic acid is too high to be economically competitive with the petrochemical-based products. Itaconic acid is generally produced from raw corn starch, including three steps: enzymatic hydrolysis of corn starch into a glucose-rich syrup by α-amylase and glucoamylase, fermentation, and recovery of itaconic acid. The whole process is very time-consuming and energy-intensive.

Results

In order to reduce the production cost, saccharification and fermentation were integrated into one step through overexpressing the glucoamylase gene in A. terreus under the control of the native PcitA promoter. The transformant XH61-5 produced higher itaconate titer from liquefied starch than WT. To further increase the titer by enhancing the secretion capacity of overexpressed glucoamylase, a stronger signal peptide was selected based on the major secreted protein ATEG_02176 (an acid phosphatase precursor) by A. terreus under the itaconate production conditions. Under the control of the stronger signal peptide, the transformant XH86-8 showed higher itaconate production level than XH61-5 from liquefied starch. The itaconate titer was further enhanced through a two-step process involving the vegetative and production phase, and the transformant XH86-8 produced comparable itaconate titer from liquefied starch to current one (~80 g/L) from saccharified starch hydrolysates in industry. The effects of the new signal peptide and the two-step process on itaconate production were investigated and discussed.

Conclusions

Itaconic acid could be efficiently produced from liquefied corn starch by overexpressing the glucoamylase gene in A. terreus, which will be helpful for constructing a highly efficient microbial cell factory for itaconate production and for further lowering the production cost of itaconic acid.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-014-0108-1) contains supplementary material, which is available to authorized users.

Improving itaconic acid production through genetic engineering of an industrial Aspergillus terreus strain

Background

Itaconic acid, which has been declared to be one of the most promising and flexible building blocks, is currently used as monomer or co-monomer in the polymer industry, and produced commercially by Aspergillus terreus. However, the production level of itaconic acid hasn’t been improved in the past 40 years, and mutagenesis is still the main strategy to improve itaconate productivity. The genetic engineering approach hasn’t been applied in industrial A. terreus strains to increase itaconic acid production.

Results

In this study, the genes closely related to itaconic acid production, including cadA, mfsA, mttA, ATEG_09969, gpdA, ATEG_01954, acoA, mt-pfkA and citA, were identified and overexpressed in an industrial A. terreus strain respectively. Overexpression of the genes cadA (cis-aconitate decarboxylase) and mfsA (Major Facilitator Superfamily Transporter) enhanced the itaconate production level by 9.4% and 5.1% in shake flasks respectively. Overexpression of other genes showed varied effects on itaconate production. The titers of other organic acids were affected by the introduced genes to different extent.

Conclusions

Itaconic acid production could be improved through genetic engineering of the industrially used A. terreus strain. We have identified some important genes such as cadA and mfsA, whose overexpression led to the increased itaconate productivity, and successfully developed a strategy to establish a highly efficient microbial cell factory for itaconate protuction. Our results will provide a guide for further enhancement of the itaconic acid production level through genetic engineering in future.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-014-0119-y) contains supplementary material, which is available to authorized users.

Cloning, characterization and application of a glyceraldehyde-3-phosphate dehydrogenase promoter from Aspergillus terreus

It is important to develop native and highly efficient promoters for effective genetic engineering of filamentous fungi. Although Aspergillus terreus is an important industrial fungus for the production of itaconic acid and lovastatin, the available genetic toolbox for this microorganism is still rather limited. We have cloned the 5′ upstream region of the glyceraldehyde-3-phosphate dehydrogenase gene (gpd; 2,150 bp from the start codon) from A. terreus CICC 40205 and subsequently confirmed its promoter function using sgfp (synthetic green fluorescent protein) as the reporter. The sequence of the promoter PgpdAt was further analysed by systematic deletion to obtain an effective and compact functional promoter. Two truncated versions of PgpdAt (1,081 and 630 bp) were also able to drive sgfp expression in A. terreus. The activities of these three PgpdAt promoters of varying different lengths were further confirmed by fluorescence, western blot and transcription. The shortest one (630 bp) was successfully applied as a driver of vgb expression in the genetic engineering of A. terreus. The function of expressed haemoglobin was demonstrated by the CO (carbon monoxide)-difference spectrum and enhanced oxygen uptake rate, glucose consumption and itaconic acid titer. Our study was successful in developing and validating an efficient and compact native promoter for genetic engineering of A. terreus.

Expression of the Aspergillus terreus itaconic acid biosynthesis cluster in Aspergillus niger

Background

Aspergillus terreus is a natural producer of itaconic acid and is currently used to produce itaconic acid on an industrial scale. The metabolic process for itaconic acid biosynthesis is very similar to the production of citric acid in Aspergillus niger. However, a key enzyme in A. niger, cis-aconitate decarboxylase, is missing. The introduction of the A. terreus cadA gene in A. niger exploits the high level of citric acid production (over 200 g per liter) and theoretically can lead to production levels of over 135 g per liter of itaconic acid in A. niger. Given the potential for higher production levels in A. niger, production of itaconic acid in this host was investigated.

Results

Expression of Aspergillus terreus cis-aconitate decarboxylase in Aspergillus niger resulted in the production of a low concentration (0.05 g/L) of itaconic acid. Overexpression of codon-optimized genes for cis-aconitate decarboxylase, a mitochondrial transporter and a plasma membrane transporter in an oxaloacetate hydrolase and glucose oxidase deficient A. niger strain led to highly increased yields and itaconic acid production titers. At these higher production titers, the effect of the mitochondrial and plasma membrane transporters was much more pronounced, with levels being 5–8 times higher than previously described.

Conclusions

Itaconic acid can be produced in A. niger by the introduction of the A. terreus cis-aconitate decarboxylase encoding cadA gene. This results in a low itaconic acid production level, which can be increased by codon-optimization of the cadA gene for A. niger. A second crucial requirement for efficient production of itaconic acid is the expression of the A. terreus mttA gene, encoding a putative mitochondrial transporter. Expression of this transporter results in a twenty-fold increase in the secretion of itaconic acid. Expression of the A. terreus itaconic acid cluster consisting of the cadA gene, the mttA gene and the mfsA gene results in A. niger strains that produce over twenty five-fold higher levels of itaconic acid and show a twenty-fold increase in yield compared to a strain expressing only CadA.