Effects of heterologous expression of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase on organic acid production in Aspergillus carbonarius

A Review on the Production of C4 Platform Chemicals from Biochemical Conversion of Sugar Crop Processing Products and By-Products

The development and commercialization of sustainable chemicals from agricultural products and by-products is necessary for a circular economy built on renewable natural resources. Among the largest contributors to the final cost of a biomass conversion product is the cost of the initial biomass feedstock, representing a significant challenge in effective biomass utilization. Another major challenge is in identifying the correct products for development, which must be able to satisfy the need for both low-cost, drop-in fossil fuel replacements and novel, high-value fine chemicals (and/or commodity chemicals). Both challenges can be met by utilizing wastes or by-products from biomass processing, which have very limited starting cost, to yield platform chemicals. Specifically, sugar crop processing (e.g., sugarcane, sugar beet) is a mature industry that produces high volumes of by-products with significant potential for valorization. This review focuses specifically on the production of acetoin (3-hydroxybutanone), 2,3-butanediol, and C4 dicarboxylic (succinic, malic, and fumaric) acids with emphasis on biochemical conversion and targeted upgrading of sugar crop products/by-products. These C4 compounds are easily derived from fermentations and can be converted into many different final products, including food, fragrance, and cosmetic additives, as well as sustainable biofuels and other chemicals. State-of-the-art literature pertaining to optimization strategies for microbial conversion of sugar crop byproducts to C4 chemicals (e.g., bagasse, molasses) is reviewed, along with potential routes for upgrading and valorization. Directions and opportunities for future research and industrial biotechnology development are discussed.

Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass

BACKGROUND

Succinic acid has great potential to be a new bio-based building block for deriving a number of value-added chemicals in industry. Bio-based succinic acid production from renewable biomass can provide a feasible approach to partially alleviate the dependence of global manufacturing on petroleum refinery. To improve the economics of biological processes, we attempted to explore possible solutions with a fungal cell platform. In this study, Aspergillus niger, a well-known industrial production organism for bio-based organic acids, was exploited for its potential for succinic acid production.

RESULTS

With a ribonucleoprotein (RNP)-based CRISPR-Cas9 system, consecutive genetic manipulations were realized in engineering of the citric acid-producing strain A. niger ATCC 1015. Two genes involved in production of two byproducts, gluconic acid and oxalic acid, were disrupted. In addition, an efficient C₄-dicarboxylate transporter and a soluble NADH-dependent fumarate reductase were overexpressed. The resulting strain SAP-3 produced 17 g/L succinic acid while there was no succinic acid detected at a measurable level in the wild-type strain using a synthetic substrate. Furthermore, two cultivation parameters, temperature and pH, were investigated for their effects on succinic acid production. The highest amount of succinic acid was obtained at 35 °C after 3 days, and low culture pH had inhibitory effects on succinic acid production. Two types of renewable biomass were explored as substrates for succinic acid production. After 6 days, the SAP-3 strain was capable of producing 23 g/L and 9 g/L succinic acid from sugar beet molasses and wheat straw hydrolysate, respectively.

CONCLUSIONS

In this study, we have successfully applied the RNP-based CRISPR-Cas9 system in genetic engineering of A. niger and significantly improved the succinic acid production in the engineered strain. The studies on cultivation parameters revealed the impacts of pH and temperature on succinic acid production and the future challenges in strain development. The feasibility of using renewable biomass for succinic acid production by A. niger has been demonstrated with molasses and wheat straw hydrolysate.

Disruption and overexpression of 6-phosphofructo-2-kinase influence organic acid production in Aspergillus carbonarius ITEM 5010

Aspergillus carbonarius is an efficient producer of organic acids with great potential for bio-based production of organic acids. In this study, we identified a gene f2kp encoding the enzyme 6-phosphofructo-2-kinase known as an allosteric regulator of the glycolytic flux and investigated its role in the production of organic acid. The strategy was to examine the impact of citric acid and malic acid production by overexpressing and disrupting f2kp, respectively. The overexpressing transformants expressed f2kp at higher level than the wild type, whereas no expression of f2kp was detected in the knockout transformants. Citric acid and malic acid production by the knockout strains decreased sharply along with a significant lower sugar consumption, though the overexpressing transformants produced similar amounts of citric acid and malic acid as the wild type. We conclude that 6-phosphofructo-2-kinase has an important regulatory role for the glycolytic flux and organic acid production in A. carbonarius.

Sugar-regulated susceptibility of tomato fruit to Colletotrichum and Penicillium requires differential mechanisms of pathogenicity and fruit responses

Colletotrichum gloeosporioides and Penicillium expansum cause postharvest diseases in tropical and deciduous fruit. During colonization, C. gloeosporioides and P. expansum secrete ammonia in hosts with low sugar content (LowSC) and gluconic acid in hosts with high sugar content (HighSC), respectively, as a mechanism to modulate enhanced pathogenicity. We studied the pathogens interactions with tomato lines of similar genetic background but differing in their sugar content. Colletotrichum gloeosporioides showed enhanced colonization of the LowSC line with differential expression response of 15% of its genes including enhanced relative expression of glycosyl hydrolases, glucanase and MFS-transporter genes. Enhanced colonization of P. expansum occurred in the HighSC line, accompanied by an increase in carbohydrate metabolic processes mainly phosphoenolpyruvate carboxykinase, and only 4% of differentially expressed genes. Gene response of the two host lines strongly differed depending on the sugar level. Limited colonization of HighSC line by C. gloeosporioides was accompanied by a marked alteration of gene expression compared the LowSC response to the same pathogen; while colonization by P. expansum resulted in a similar response of the two different hosts. We suggest that this differential pattern of fungal/host responses may be the basis for the differential of host range of both pathogens in nature.

Fusarium virguliform e Transcriptional Plasticity Is Revealed by Host Colonization of Maize versus Soybean

We exploited the broad host range of Fusarium virguliforme to identify differential fungal responses leading to either an endophytic or a pathogenic lifestyle during colonization of maize (Zea mays) and soybean (Glycine max), respectively. To provide a foundation to survey the transcriptomic landscape, we produced an improved de novo genome assembly and annotation of F. virguliforme using PacBio sequencing. Next, we conducted a high-resolution time course of F. virguliforme colonization and infection of both soybean, a symptomatic host, and maize, an asymptomatic host. Comparative transcriptomic analyses uncovered a nearly complete network rewiring, with less than 8% average gene coexpression module overlap upon colonizing the different plant hosts. Divergence of transcriptomes originating from host specific temporal induction genes is central to infection and colonization, including carbohydrate-active enzymes (CAZymes) and necrosis inducing effectors. Upregulation of Zn(II)-Cys6 transcription factors were uniquely induced in soybean at 2 d postinoculation, suggestive of enhanced pathogen virulence on soybean. In total, the data described herein suggest that F. virguliforme modulates divergent infection profiles through transcriptional plasticity.

Disruption of a putative mitochondrial oxaloacetate shuttle protein in Aspergillus carbonarius results in secretion of malic acid at the expense of citric acid production

BACKGROUND

In filamentous fungi, transport of organic acids across the mitochondrial membrane is facilitated by active transport via shuttle proteins. These transporters may transfer different organic acids across the membrane while taking others the opposite direction. In Aspergillus niger, accumulation of malate in the cytosol can trigger production of citric acid via the exchange of malate and citrate across the mitochondrial membrane. Several mitochondrial organic acid transporters were recently studied in A. niger showing their effects on organic acid production.

RESULTS

In this work, we studied another citric acid producing fungus, Aspergillus carbonarius, and identified by genome-mining a putative mitochondrial transporter MtpA, which was not previously studied, that might be involved in production of citric acid. This gene named mtpA encoding a putative oxaloacetate transport protein was expressed constitutively in A. carbonarius based on transcription analysis. To study its role in organic acid production, we disrupted the gene and analyzed its effects on production of citric acid and other organic acids, such as malic acid. In total, 6 transformants with gene mtpA disrupted were obtained and they showed secretion of malic acid at the expense of citric acid production.

CONCLUSION

A putative oxaloacetate transporter gene which is potentially involved in organic acid production by A. carbonarius was identified and further investigated on its effects on production of citric acid and malic acid. The mtpA knockout strains obtained produced less citric acid and more malic acid than the wild type, in agreement with our original hypothesis. More extensive studies should be conducted in order to further reveal the mechanism of organic acid transport as mediated by the MtpA transporter.

Enhancement of malate production through engineering of the periplasmic rTCA pathway in Escherichia coli

The compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency; however, prokaryotes are unicellular organisms that lack membrane-bound organelles. To mimic this natural compartmentalization, we present here the targeting of the reductive tricarboxylic acid (rTCA) pathway to the periplasm to enhance the production of malate. A multigene combination knockout strategy was used to construct a phosphoenolpyruvate (PEP) pool. Then, the genes encoding phosphoenolpyruvate carboxykinase and malate dehydrogenase were combinatorially overexpressed to construct a cytoplasmic rTCA pathway for malate biosynthesis; however, the efficiency of malate production was low. To further enhance malate production, the rTCA pathway was targeted to the periplasm, which led to a 100% increase in malate production to 18.8 mM. Next, dual metabolic engineering regulation was adopted to balance the cytoplasmic and periplasmic pathways, leading to an increase in malate production to 58.8 mM. The final engineered strain, GL2306, produced 193 mM malate with a yield of 0.53 mol/mol in 5 L of pH-stat fed-batch culture. The strategy described here paves the way for the development of metabolic engineering and synthetic biology in the microbial production of chemicals.

Alkane biosynthesis by Aspergillus carbonarius ITEM 5010 through heterologous expression of Synechococcus elongatus acyl-ACP/CoA reductase and aldehyde deformylating oxygenase genes

In this study we describe the heterologous expression of the recently identified cyanobacterial pathway for long chain alkane biosynthesis, involving the reduction of fatty acyl-ACP to fatty aldehyde and the subsequent conversion of this into alkanes, in the filamentous fungus Aspergillus carbonarius ITEM 5010. Genes originating from Synechococcus elongatus strain PCC7942, encoding acyl-ACP/CoA reductase and aldehyde deformylating oxygenase enzymes, were successfully expressed in A. carbonarius, which lead to the production of pentadecane and heptadecane, alkanes that have not been previously produced by this fungus. Titers of 0.2, 0.5 and 2.7 mg/l pentadecane and 0.8, 1.6 and 10.2 mg/l heptadecane were achieved using glucose, Yeast malt and oatmeal media, respectively. Besides producing alkanes, we found elevated levels of internal free fatty acids and triglycerides in the alkane producing transformant. These findings can indicate that a yet unidentified, native fatty aldehyde dehydrogenase channels back the fatty aldehydes into the fatty acid metabolism, thus competing for substrate with the heterologously expressed fatty aldehyde deformylating oxygenase. These findings will potentially facilitate the future application of robust, fungal cell factories for the production of advanced biofuels from various substrates.

Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi-guided multiplexed metabolic tuning

The application of rational design in reallocating metabolic flux to overproduce desired chemicals is always restricted by the native regulatory network. Here, we demonstrated that in vitro modular pathway optimization combined with in vivo multiplexed combinatorial engineering enables effective characterization of the bottleneck of a complex biosynthetic cascade and improves the output of the engineered pathway. As a proof of concept, we systematically identified the rate-limiting step of a five-gene malate biosynthetic pathway by combinatorially tuning the enzyme loads of a reconstituted biocatalytic reaction in a cell-free system. Using multiplexed CRISPR interference, we subsequently eliminated the metabolic constraints by rationally assigning an optimal gene expression pattern for each pathway module. The present engineered strain Escherichia coli B0013-47 exhibited a 2.3-fold increase in malate titer compared with that of the parental strain, with a yield of 0.85 mol/mol glucose in shake-flask culture and titer of 269 mM (36 g/L) in fed-batch cultivation. The strategy reported herein represents a powerful method for improving the efficiency of multi-gene pathways and advancing the success of metabolic engineering.

Overexpression of a C4-dicarboxylate transporter is the key for rerouting citric acid to C4-dicarboxylic acid production in Aspergillus carbonarius

Background

C₄-dicarboxylic acids, including malic acid, fumaric acid and succinic acid, are valuable organic acids that can be produced and secreted by a number of microorganisms. Previous studies on organic acid production by Aspergillus carbonarius, which is capable of producing high amounts of citric acid from varieties carbon sources, have revealed its potential as a fungal cell factory. Earlier attempts to reroute citric acid production into C₄-dicarboxylic acids have been with limited success.

Results

In this study, a glucose oxidase deficient strain of A. carbonarius was used as the parental strain to overexpress a native C₄-dicarboxylate transporter and the gene frd encoding fumarate reductase from Trypanosoma brucei individually and in combination. Impacts of the introduced genetic modifications on organic acid production were investigated in a defined medium and in a hydrolysate of wheat straw containing high concentrations of glucose and xylose. In the defined medium, overexpression of the C₄-dicarboxylate transporter alone and in combination with the frd gene significantly increased the production of C₄-dicarboxylic acids and reduced the accumulation of citric acid, whereas expression of the frd gene alone did not result in any significant change of organic acid production profile. In the wheat straw hydrolysate after 9 days of cultivation, similar results were obtained as in the defined medium. High amounts of malic acid and succinic acid were produced by the same strains.

Conclusions

This study demonstrates that the key to change the citric acid production into production of C₄-dicarboxylic acids in A. carbonarius is the C₄-dicarboxylate transporter. Furthermore it shows that the C₄-dicarboxylic acid production by A. carbonarius can be further increased via metabolic engineering and also shows the potential of A. carbonarius to utilize lignocellulosic biomass as substrates for C₄-dicarboxylic acid production.

Biotechnological route for sustainable succinate production utilizing oil palm frond and kenaf as potential carbon sources

Due to the world's dwindling energy supplies, greater thrust has been placed on the utilization of renewable resources for global succinate production. Exploration of such biotechnological route could be seen as an act of counterbalance to the continued fossil fuel dominance. Malaysia being a tropical country stands out among many other nations for its plenty of resources in the form of lignocellulosic biomass. To date, oil palm frond (OPF) contributes to the largest fraction of agricultural residues in Malaysia, while kenaf, a newly introduced fiber crop with relatively high growth rate, holds great potential for developing sustainable succinate production, apart from OPF. Utilization of non-food, inexhaustible, and low-cost derived biomass in the form of OPF and kenaf for bio-based succinate production remains largely untapped. Owing to the richness of carbohydrates in OPF and kenaf, bio-succinate commercialization using these sources appears as an attractive proposition for future sustainable developments. The aim of this paper was to review some research efforts in developing a biorefinery system based on OPF and kenaf as processing inputs. It presents the importance of the current progress in bio-succinate commercialization, in addition to describing the potential use of different succinate production hosts and various pretreatments-saccharifications under development for OPF and kenaf. Evaluations on the feasibility of OPF and kenaf as fermentation substrates are also discussed.

A comparison of Agrobacterium-mediated transformation and protoplast-mediated transformation with CRISPR-Cas9 and bipartite gene targeting substrates, as effective gene targeting tools for Aspergillus carbonarius

In recent years, versatile genetic tools have been developed and applied to a number of filamentous fungi of industrial importance. However, the existing techniques have limitations when it comes to achieve the desired genetic modifications, especially for efficient gene targeting. In this study, we used Aspergillus carbonarius as a host strain due to its potential as a cell factory, and compared three gene targeting techniques by disrupting the ayg1 gene involved in the biosynthesis of conidial pigment in A. carbonarius. The absence of the ayg1 gene leads to phenotypic change in conidia color, which facilitated the analysis on the gene targeting frequency. The examined transformation techniques included Agrobacterium-mediated transformation (AMT) and protoplast-mediated transformation (PMT). Furthermore, the PMT for the disruption of the ayg1 gene was carried out with bipartite gene targeting fragments and the recently adapted CRISPR-Cas9 system. All three techniques were successful in generating Δayg1 mutants, but showed different efficiencies. The most efficient method for gene targeting was AMT, but further it was shown to be dependent on the choice of Agrobacterium strain. However, there are different advantages and disadvantages of all three gene targeting methods which are discussed, in order to facilitate future approaches for fungal strain improvements.

Co-consumption of glucose and xylose for organic acid production by Aspergillus carbonarius cultivated in wheat straw hydrolysate

Aspergillus carbonarius exhibits excellent abilities to utilize a wide range of carbon sources and to produce various organic acids. In this study, wheat straw hydrolysate containing high concentrations of glucose and xylose was used for organic acid production by A. carbonarius. The results indicated that A. carbonarius efficiently co-consumed glucose and xylose and produced various types of organic acids in hydrolysate adjusted to pH 7. The inhibitor tolerance of A. carbonarius to the hydrolysate at different pH values was investigated and compared using spores and recycled mycelia. This comparison showed a slight difference in the inhibitor tolerance of the spores and the recycled mycelia based on their growth patterns. Moreover, the wild-type and a glucose oxidase deficient (Δgox) mutant were compared for their abilities to produce organic acids using the hydrolysate and a defined medium. The two strains showed a different pattern of organic acid production in the hydrolysate where the Δgox mutant produced more oxalic acid but less citric acid than the wild-type, which was different from the results obtained in the defined medium This study demonstrates the feasibility of using lignocellulosic biomass for the organic acid production by A. carbonarius.