Characterizing MttA as a mitochondrial cis-aconitic acid transporter by metabolic engineering

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.

Improved consolidated bioprocessing for itaconic acid production by simultaneous optimization of cellulase and metabolic pathway of Neurospora crassa

Lignocellulose was directly used in itaconic acid production by a model filamentous fungus Neurospora crassa. The promoters of two clock control genes and cellobiohydrolase 1 gene were selected for heterologous genes expression by evaluating different types of promoters. The effect of overexpression of different cellulase was compared, and it was found that expression of cellobiohydrolase 2 from Trichoderma reesei increased the filter paper activity by 2 times, the cellobiohydrolase activity by 4.5 times, and that the itaconic acid titer was also significantly improved. A bidirectional cis-aconitic acid accumulation strategy was established by constructing the reverse glyoxylate shunt and expressing the transporter MTTA, which increased itaconic acid production to 637.2 mg/L. The simultaneous optimization of cellulase and metabolic pathway was more conducive to the improvement of cellulase activity than that of cellulase alone, so as to further increase itaconic acid production. Finally, through the combination of fermentation by optimized strains and medium optimization, the titers of itaconic acid using Avicel and corn stover as substrate were 1165.1 mg/L and 871.3 mg/L, respectively. The results prove the potential of the consolidated bioprocessing that directly converts lignocellulose to itaconic acid by a model cellulase synthesizing strain.

Metabolomics reveals the impact of nitrogen combined with the zinc supply on zinc availability in calcareous soil via root exudates of winter wheat (Triticum aestivum)

A possible mechanism for the improved availability of zinc (Zn) in soil by combining nitrogen (N) with Zn supply was investigated based on the root exudates of winter wheat. N, Zn supply as well as their combination significantly regulated nine root exudates in winter wheat; in which, the secretion of cis-aconitic acid involving in the TCA cycle, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism and 2-oxocarboxylic acid metabolism was upregulated by N, Zn supply as well as their combination. N-Zn combination induced the activities of citrate synthase and cis-aconitase in roots and shoots of winter wheat thus to increase the concentrations of citric and aconitic acid; the decrease of isocitric acid concentrations in shoots indicated the inhibited conversion of aconitic acid to isocitric acid by N-Zn combination. It revealed a possible reason for the enhanced secretion of cis-aconitic acid by N-Zn combination. Exogenous addition of 10 μ plant-1 cis-aconitate significantly increased available Zn concentrations in soil and Zn concentrations in winter wheat under N-Zn combination. Thus, the N-Zn combination regulated the metabolism of cis-aconitic acid in winter wheat, thus enhancing the secretion of cis-aconitic acid to increase the bioavailability of Zn in soil.

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.

Effect of itaconic acid production on Neurospora crassa in consolidated bioprocessing of cellulose

A system for itaconic acid synthesis from cellulose by Neurospora crassa was established, resulting in the highest yield of itaconic acid was 354.08 + 35.99 mg/L. Meanwhile, cellulase activity increased significantly, without any strain modifications for improved cellulase production. Multi-omics analyses showed that itaconic acid synthesis reduced energy production, leading to decreases in trehalose, cell wall, fatty acids synthesis and downregulations in MAPK signaling pathway, cell cycle and meiosis. More importantly, the low-energy environment enhanced the energy-efficient cellobionic acid/gluconic acid pathway, and the cellulase composition also changed significantly, manifested as the up-regulation of LPMOs and the down-regulation of β-glucosidases. Enhancing LPMOs-cellobionic acid/gluconic acid system has the potential to reduce energy consumption of the consolidated bioprocessing. These findings offer an overview of resource allocations by N. crassa in response to itaconic acid synthesis and highlight a series of intriguing connections between itaconic acid synthesis and cellulase synthesis in consolidated bioprocessing.

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.

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.

Metabolic engineering of Schizosaccharomyces pombe for itaconic acid production

The economical production of value-added chemicals from renewable biomass is a promising aspect of producing a sustainable economy. Itaconic acid (IA) is a high value-added compound that is expected to be an alternative to petroleum-based chemicals. In this study, we developed a metabolic engineering strategy for the large-scale production of IA from glucose using the fission yeast Schizosaccharomyces pombe. Heterologous expression of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus, which encodes cis-aconitate decarboxylase in the cytosol, led to the production of 0.132 g/L of IA. We demonstrated that mitochondrial localization of CAD enhanced the production of IA. To prevent the leakage of carbon flux from the TCA cycle, we generated a strain in which the endogenous malate exporter, citrate lyase, and citrate transporter genes were disrupted. A titer of 1.110 g/L of IA was obtained from a culture of this strain started with 50 g/L of glucose. By culturing the multiple mutant strain at increased cell density, we succeeded in enhancing the IA production to 1.555 g/L. The metabolic engineering strategies presented in this study have the potential to improve the titer of the biosynthesis of derivatives of intermediates of the TCA cycle.

Transporter Engineering in Microbial Cell Factory Boosts Biomanufacturing Capacity

Microbial cell factories (MCFs) are typical and widely used platforms in biomanufacturing for designing and constructing synthesis pathways of target compounds in microorganisms. In MCFs, transporter engineering is especially significant for improving the biomanufacturing efficiency and capacity through enhancing substrate absorption, promoting intracellular mass transfer of intermediate metabolites, and improving transmembrane export of target products. This review discusses the current methods and strategies of mining and characterizing suitable transporters and presents the cases of transporter engineering in the production of various chemicals in MCFs.

Optogenetics Illuminates Applications in Microbial Engineering

Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe-host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Finally, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Aconitic Acid Recovery from Renewable Feedstock and Review of Chemical and Biological Applications

Aconitic acid (propene-1,2,3-tricarboxylic acid) is the most prevalent 6-carbon organic acid that accumulates in sugarcane and sweet sorghum. As a top value-added chemical, aconitic acid may function as a chemical precursor or intermediate for high-value downstream industrial and biological applications. These downstream applications include use as a bio-based plasticizer, cross-linker, and the formation of valuable and multi-functional polyesters that have also been used in tissue engineering. Aconitic acid also plays various biological roles within cells as an intermediate in the tricarboxylic acid cycle and in conferring unique survival advantages to some plants as an antifeedant, antifungal, and means of storing fixed pools of carbon. Aconitic acid has also been reported as a fermentation inhibitor, anti-inflammatory, and a potential nematicide. Since aconitic acid can be sustainably sourced from renewable, inexpensive sources such as sugarcane, molasses, and sweet sorghum syrup, there is enormous potential to provide multiple streams of additional income to the sugar industry through downstream industrial and biological applications that we discuss in this review.

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.

CRISPR interference-guided modulation of glucose pathways to boost aconitic acid production in Escherichia coli

Background

One major mission of microbial breeding is high-level production of desired metabolites. Overproduction of intermediate metabolites in core pathways is challenging as it may impair cell growth and viability.

Results

Here we report that aconitic acid, an intermediate metabolite in tricarboxylic acid (TCA) cycle, can be overproduced by an engineered CRISPR interference (CRISPRi) system in Escherichia coli. This CRISPRi system was designed to simultaneously target pyruvate kinase (PK) and isocitrate dehydrogenase (IDH), two enzymes in glycolytic pathway and TCA cycle, respectively. Reverse transcription and quantitative PCR and enzyme activity assays showed that this engineered CRISPRi system significantly repressed the genes encoding IDH and PK, resulting in simultaneous reduction in the activities of IDH and PK. In shake-flask and fed-batch cultivation, this CRISPRi strain produced 60-fold (362.80 ± 22.05 mg/L) and 15-fold (623.80 ± 20.05 mg/L) of aconitic acid relative to the control strain, respectively. In addition, this two-target CRISPRi strain maintained low levels of acetate and lactate, two problematic byproducts.

Conclusions

This work demonstrates that CRISPRi system can improve aconitic acid production by coordinating glycolysis and TCA cycle. This study provides insights for high-level production of the intermediate metabolites in central pathways.

Transporter Engineering for Microbial Manufacturing

Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.

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.

Metabolic engineering of an acid-tolerant yeast strain Pichia kudriavzevii for itaconic acid production

Itaconic acid (IA), or 2-methylenesuccinic acid, has a broad spectrum of applications in the biopolymer industry owing to the presence of one vinyl bond and two acid groups in the structure. Its polymerization can follow a similar mechanism as acrylic acid but additional functionality can be incorporated into the extra beta acid group. Currently, the bio-based production of IA in industry relies on the fermentation of the filamentous fungus Aspergillus terreus. However, the difficulties associated with the fermentation undertaken by filamentous fungi together with the pathogenic potential of A. terreus pose a serious challenge for industrial-scale production. In recent years, there has been increasing interest in developing alternative production hosts for fermentation processes that are more homogenous in the production of organic acids.

Pichia kudriavzevii is a non-conventional yeast with high acid tolerance to organic acids at low pH, which is a highly desirable trait by easing downstream processing. We introduced cis-aconitic acid decarboxylase gene (cad) from A. terreus (designated At_cad) into this yeast and established the initial titer of IA at 135 ​± ​5 ​mg/L. Subsequent overexpression of a native mitochondrial tricarboxylate transporter (herein designated Pk_mttA) presumably delivered cis-aconitate efficiently to the cytosol and doubled the IA production. By introducing the newly invented CRISPR-Cas9 system into P. kudriavzevii, we successfully knocked out both copies of the gene encoding isocitrate dehydrogenase (ICD), aiming to increase the availability of cis-aconitate. The resulting P. kudriavzevii strain, devoid of ICD and overexpressing Pk_mttA and At_cad on its genome produced IA at 505 ​± ​17.7 ​mg/L in shake flasks, and 1232 ​± ​64 ​mg/L in fed-batch fermentation. Because the usage of an acid-tolerant species does not require pH adjustment during fermentation, this work demonstrates the great potential of engineering P. kudriavzevii as an industrial chassis for the production of organic acid.

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Pichia kudriavzevii is a non-conventional yeast with high acid tolerance to organic acids at low pH.

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Engineering P. kudriavzevii to produce itaconic acid, a highly sought after biopolymer precursor.

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First description of a cis-aconitic acid transporter identified from a host besides the native producer of itaconic acid.

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Discussion on the potential of P. kudriavzevii as an industrial chassis for the production of organic acids.

Advanced strategy for metabolite exploration in filamentous fungi

Filamentous fungi comprise an abundance of gene clusters that encode high-value metabolites, whereas affluent gene clusters remain silent during laboratory conditions. Complex cellular metabolism further limits these metabolite yields. Therefore, diverse strategies such as genetic engineering and chemical mutagenesis have been developed to activate these cryptic pathways and improve metabolite productivity. However, lower efficiencies of gene modifications and screen tools delayed the above processes. To address the above issues, this review describes an alternative design-construction evaluation optimization (DCEO) approach. The DCEO tool provides theoretical and practical principles to identify potential pathways, modify endogenous pathways, integrate exogenous pathways, and exploit novel pathways for their diverse metabolites and desirable productivities. This DCEO method also offers different tactics to balance the cellular metabolisms, facilitate the genetic engineering, and exploit the scalable metabolites in filamentous fungi.

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.

Decrease of citric acid produced by Aspergillus niger through disruption of the gene encoding a putative mitochondrial citrate-oxoglutarate shuttle protein

The transporter that exports citric acid (CA) generated in mitochondria to the cytosol is an important component of the CA production machinery of Aspergillus niger. In this report, we cloned and identified the gene cocA, encoding a 33.7-kDa putative mitochondrial citrate-oxoglutarate shuttle protein of the CA hyper-producer A. niger WU-2223L. The amount of CA produced by a representative cocA disruptant (35 g/L) was significantly lower than that produced by strain WU-2223L (63 g/L) after culture for 12 days under CA production conditions, and the phenotype of the cocA disruptant differed in part from that of strain WU-2223L. A cocA disruptant complemented with cocA exhibited the same phenotypes as those of strain WU-2223L. This report is the first to show that cocA and its protein product clearly contribute to substantial CA production by A. niger, and provides a significant insight into microbial organic acid production by fermentation.

Abbreviations: CA: citric acid; CD medium: Czapek-Dox medium; CS: citrate synthase; CTP: citrate transport protein; HR: homologous recombination; MCF: mitochondrial carrier family; RT-PCR: reverse-transcription PCR; TCA: tricarboxylic acid

Synergistic Rewiring of Carbon Metabolism and Redox Metabolism in Cytoplasm and Mitochondria of Aspergillus oryzae for Increased l-Malate Production

l-Malate is an important platform chemical that has extensive applications in the food, feed, and wine industries. Here, we synergistically engineered the carbon metabolism and redox metabolism in the cytosol and mitochondria of a previously engineered Aspergillus oryzae to further improve the l-malate titer and decrease the byproduct succinate concentration. First, the accumulation of the intermediate pyruvate was eliminated by overexpressing a pyruvate carboxylase from Rhizopus oryzae in the cytosol and mitochondria of A. oryzae, and consequently, the l-malate titer increased 7.5%. Then, malate synthesis via glyoxylate bypass in the mitochondria was enhanced, and citrate synthase in the oxidative TCA cycle was downregulated by RNAi, enhancing the l-malate titer by 10.7%. Next, the exchange of byproducts (succinate and fumarate) between the cytosol and mitochondria was regulated by the expression of a dicarboxylate carrier Sfc1p from Saccharomyces cerevisiae in the mitochondria, which increased l-malate titer 3.5% and decreased succinate concentration 36.8%. Finally, an NADH oxidase from Lactococcus lactis was overexpressed to decrease the NADH/NAD⁺ ratio, and the engineered A. oryzae strain produced 117.2 g/L l-malate and 3.8 g/L succinate, with an l-malate yield of 0.9 g/g corn starch and a productivity of 1.17 g/L/h. Our results showed that synergistic engineering of the carbon and redox metabolisms in the cytosol and mitochondria of A. oryzae effectively increased the l-malate titer, while simultaneously decreasing the concentration of the byproduct succinate. The strategies used in our work may be useful for the metabolic engineering of fungi to produce other industrially important chemicals.

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.

An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger

Metabolic engineering requires functional genetic tools for easy and quick generation of multiple pathway variants. A genetic engineering toolbox for A. niger is presented, which facilitates the generation of strains carrying heterologous expression cassettes at a defined genetic locus. The system is compatible with Golden Gate cloning, which facilitates the DNA construction process and provides high design flexibility. The integration process is mediated by a CRISPR/Cas9 strategy involving the cutting of both the genetic integration locus (pyrG) as well as the integrating plasmid. Only a transient expression of Cas9 is necessary and the carrying plasmid is readily lost using a size-reduced AMA1 variant. A high integration efficiency into the fungal genome of up to 100% can be achieved, thus reducing the screening process significantly. The feasibility of the approach was demonstrated by the integration of an expression cassette enabling the production of aconitic acid in A. niger.

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.

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.

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.

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.

Transporter and its engineering for secondary metabolites

Secondary metabolites possess a lot of biological activities, and to achieve their functions, transmembrane transportation is crucial. Elucidation of their transport mechanisms in the cell is critical for discovering ways to improve the production. Here, we have summarized the recent progresses for representative secondary metabolite transporters and also the strategies for uncovering the transporter systems in plants and microbes. We have also discussed the transporter engineering strategies being utilized for improving the heterologous natural product production, which exhibits promising future under the guide of synthetic biology.