Engineering a Phosphoketolase Pathway to Supplement Cytosolic Acetyl-CoA in Aspergillus niger Enables a Significant Increase in Citric Acid Production

Engineering Komagataella phaffii for citric acid production through carbon-conserving supply of acetyl-CoA

The oxidative formation of AcCoA limits the glycolytic pathway yield (YPGLY) for citric acid due to the NADH overflow and carbon loss as CO2. An interesting approach to enhance product yields is the incorporation of carbon-conserving pathways. This study assesses the potential of a carbon-conserving AcCoA pathway, the glycolysis alternative high carbon yield cycle (GATHCYC), to improve citric acid production, utilizing the non-native citric acid producer Komagataella phaffii as an orthogonal test system. The combination of different metabolic engineering strategies enabled K. phaffii to acquire the ability to produce extracellular citric acid. By constructing the GATHCYC in the cytosol and peroxisomes, the intracellular concentration of AcCoA increased. Overexpression of the genes encoding pyruvate carboxylase (PYC2), citrate synthase (CIT2) and citrate exporter protein (cexA) in the peroxisomal AcCoA strains boosted the citric acid production. Thus, the best producer strain reached a citric acid titer of 51.3 ± 0.9 g L-1 and a yield of 0.59 ± 0.01 g g-1 after 76 h of glucose-limited fed-batch cultivation. Our results highlight the potential of using GATHCYC to provide an efficient supply of acetyl-CoA to enhance citric acid production. This approach could be exploited for the production of other AcCoA-derived compounds of industrial relevance in different cell factories.

The role of ATP citrate lyase, phosphoketolase, and malic enzyme in oleaginous Rhodotorula toruloides

Rhodotorula toruloides is an oleaginous yeast recognized for its robustness and the production of high content of neutral lipids. Early biochemical studies have linked ATP citrate lyase (ACL), phosphoketolase (PK), and cytosolic malic enzyme (cMAE) with de novo lipid synthesis. In this study, we discovered that upon a CRISPR/Cas9-mediated knockout of the ACL gene, lipid content in R. toruloides IFO0880 decreased from 50 to 9% of its dry cell weight (DCW) in glucose medium and caused severe growth defects (reduced specific growth rate, changes in cell morphology). In xylose medium, the lipid content decreased from 43 to 38% of DCW. However, when grown on acetate as the sole carbon source, the lipid content decreased from 45 to 20% of DCW. Significant growth defects as a result of ACL knockout were observed on all substrates. In contrast, PK knockout resulted in no change in growth or lipid synthesis. Knocking out cMAE gene resulted in lipid increase of 2.9% of DCW and 23% increase in specific growth rate on glucose. In xylose or acetate medium, no change in lipid production as a result of cMAE gene knockout was observed. These results demonstrated that ACL plays a crucial role in lipid synthesis in R. toruloides IFO0880, as opposed to PK pathway or cMAE, whose presence in some conditions even disfavors lipid production. These results provided valuable information for future metabolic engineering of R. toruloides. KEY POINTS: • ACL is crucial for the fatty acid synthesis and growth in R. toruloides IFO0880. • Lipid production and cell growth is are unchanged as a result of PK knockout. • Cytosolic malic enzyme does not play a significant role in lipogenesis.

Improving glucose oxidase catalysis in Aspergillus niger via Vitreoscilla hemoglobin fusion protein

Oxygen is crucial for converting glucose to gluconic acid catalyzed by glucose oxidase (Gox). However, industrial gluconic acid production faces oxygen supply limitations. To enhance Gox efficiency, Vitreoscilla hemoglobin (VHb) has been considered as an efficient oxygen transfer carrier. This study identified GoxA, a specific isoform of Gox in the industrial gluconic acid-producing strain of Aspergillus niger. Various forms of VHb expression in A. niger were tested to improve GoxA's catalytic efficiency. Surprisingly, the expression of free VHb, both intracellularly and extracellularly, did not promote gluconic acid production during shake flask fermentation. Then, five fusion proteins were constructed by linking Gox and VHb using various methods. Among these, VHb-GS1-GoxA, where VHb's C-terminus connected to GoxA's N-terminus via the flexible linker GS1, demonstrated a significantly higher Kcat/Km value (96% higher) than GoxA. Unfortunately, the expression of VHb-GS1-GoxA in A. niger was limited, resulting in a low gluconic acid production of 3.0 g/L. To overcome the low expression problem, single- and dual-strain systems were designed with tools of SpyCatcher/SpyTag and SnoopCatcher/SnoopTag. In these systems, Gox and VHb were separately expressed and then self-assembled into complex proteins. Impressively, the single-strain system outperformed the GoxA overexpression strain S1971, resulting in 23% and 9% higher gluconic acid production under 0.6 vvm and 1.2 vvm aeration conditions in the bioreactor fermentation, respectively. The successful construction of Gox and VHb fusion or complex proteins, as proposed in this study, presents promising approaches to enhance Gox catalytic efficiency and lower aerodynamic costs in gluconic acid production. KEY POINTS: • Overexpressing free VHb in A. niger did not improve the catalytic efficiency of Gox • The VHb-GS1-GoxA showed an increased Kcat/Km value by 96% than GoxA • The single-strain system worked better in the gluconic acid bioreactor fermentation.

Transcriptomics identify the triggering of citrate export as the key event caused by manganese deficiency in Aspergillus niger

For over a century, the filamentous Ascomycete fungus Aspergillus niger has played a pivotal role in the industrial production of citric acid. A critical fermentation parameter that sustains high-yield citric acid accumulation is the suboptimal concentration of manganese(II) ions in the culture broth at the early stages of the process. However, the requirement for this deficiency has not been investigated on a functional genomics level. In this study, we compared the transcriptome of the citric acid hyper-producer A. niger NRRL2270 strain grown under citric acid-producing conditions in 6-L scale bioreactors at Mn2+ ion-deficient (5 ppb) and Mn2+ ion-sufficient (100 ppb) conditions at three early time points of cultivation. Of the 11,846 genes in the genome, 963 genes (8.1% of the total) were identified as significantly differentially expressed under these conditions. Disproportionately high number of differentially regulated genes encode predicted extracellular and membrane proteins. The most abundant gene group that was upregulated in Mn2+ ion deficiency condition encodes enzymes acting on polysaccharides. In contrast, six clusters of genes encoding secondary metabolites showed downregulation under manganese deficiency. Mn2+ deficiency also triggers upregulation of the cexA gene, which encodes the citrate exporter. We provide functional evidence that the upregulation of cexA is caused by the intracellular accumulation of citrate or acetyl-CoA and is a major factor in triggering citrate overflow.

IMPORTANCE

Citric acid is produced on industrial scale by batch fermentation of the filamentous fungus Aspergillus niger. High-yield citric acid production requires a low (<5 ppb) manganese(II) ion concentration in the culture broth. However, the requirement for this deficiency has not been investigated on a functional genomics level. Here, we compared the transcriptome of a citric acid hyper-producer A. niger strain grown under citric acid-producing conditions in 6-L scale bioreactors at Mn2+ ion-deficient (5 ppb) and Mn2+ ion-sufficient (100 ppb) conditions at three early time points of cultivation. We observed that Mn2+ deficiency triggers an upregulation of the citrate exporter gene cexA and provides functional evidence that this event is responsible for citrate overflow. In addition to the industrial relevance, this is the first study that examined the role of Mn2+ ion deficiency in a heterotrophic eukaryotic cell on a genome-wide scale.

Enhanced Citric Acid Production through Aspergillus niger: Insights from Fermentation Studies Using Sugarcane Molasses

The production of citric acid, a vital agricultural commodity utilized across various industries such as food, beverages, pharmaceuticals, agriculture, detergents, and cosmetics, predominantly relies on microbial fermentation, with Aspergillus niger accounting for approximately 90% of global production. In this study, we aimed to optimize the key factors influencing citric acid production, with a focus on strains, fermentation techniques, and carbon sources, particularly sugarcane molasses. A. niger, sourced from the Botany department/Biotechnology laboratories at Govt. College of Science, Lahore, was employed for citric acid production. The process involved inoculum preparation through spore collection from 3 to 5 days of cultured PDA slants. The fermentation medium, comprising cane molasses with a 15% sugar concentration, was meticulously prepared and optimized for various factors, including magnesium sulfate, potassium ferrocyanide, time of addition of potassium ferrocyanide, ammonium oxalate, and calcium chloride. Our optimization results shed light on the significant impact of different factors on citric acid production. For instance, the addition of 0.4 g/L magnesium sulfate led to a maximum yield of 75%, while 2 g/L potassium ferrocyanide, added at 24 h, achieved a yield of 78%. Remarkably, ammonium oxalate, at a concentration of 10 g/L, resulted in a notable 77% yield. Conversely, the addition of calcium chloride exhibited negligible effects on citric acid production, with the control group yielding more at 78%. Our study underscores the potential for optimizing factors to enhance citric acid production by A. niger in submerged fermentation. These findings highlight the pivotal role of magnesium sulfate, potassium ferrocyanide, and ammonium oxalate in augmenting citric acid yields while emphasizing the minimal impact of calcium chloride. Ultimately, these insights contribute to advancing our understanding of microbial citric acid biosynthesis, providing valuable implications for industrial applications and future research endeavors.