Overproduction of poly(β-malic acid) (PMA) from glucose by a novel Aureobasidium sp. P6 strain isolated from mangrove system

Use of Aureobasidium in a sustainable economy

Aureobasidium is omnipresent and can be isolated from air, water bodies, soil, wood, and other plant materials, as well as inorganic materials such as rocks and marble. A total of 32 species of this fungal genus have been identified at the level of DNA, of which Aureobasidium pullulans is best known. Aureobasidium is of interest for a sustainable economy because it can be used to produce a wide variety of compounds, including enzymes, polysaccharides, and biosurfactants. Moreover, it can be used to promote plant growth and protect wood and crops. To this end, Aureobasidium cells adhere to wood or plants by producing extracellular polysaccharides, thereby forming a biofilm. This biofilm provides a sustainable alternative to petrol-based coatings and toxic chemicals. This and the fact that Aureobasidium biofilms have the potential of self-repair make them a potential engineered living material avant la lettre. KEY POINTS: •Aureobasidium produces products of interest to the industry •Aureobasidium can stimulate plant growth and protect crops •Biofinish of A. pullulans is a sustainable alternative to petrol-based coatings •Aureobasidium biofilms have the potential to function as engineered living materials.

Recent advances in the production of malic acid by native fungi and engineered microbes

Malic acid is mainly produced by chemical methods which lead to various environmental sustainability concerns associated with CO₂ emissions and resulting global warming. Since malic acid is naturally synthesized, microorganisms offer an eco-friendly and cost-effective alternative for its production. An additional advantage of microbial production is the synthesis of pure L-form of malic acid. Due to its numerous applications, biotechnologically- produced L-malic acid is a much sought-after platform chemical. Malic acid can be produced by microbial fermentation via oxidative/reductive TCA and glyoxylate pathways. This article elaborates the potential and limitations of high malic acid producing native fungi belonging to Aspergillus, Penicillium, Ustilago and Aureobasidium spp. The utilization of industrial side streams and low value renewable substrates such as crude glycerol and lignocellulosic biomass is also discussed with a view to develop a competitive bio-based production process. The major impediments present in the form of toxic compounds from lignocellulosic residues or synthesized during fermentation along with their remedial measures are also described. The article also focuses on production of polymalic acid from renewable substrates which opens up a cost-cutting dimension in production of this biodegradable polymer. Finally, the recent strategies being employed for its production in recombinant organisms have also been covered.

Using Machine Learning Methods to Predict the ß-Poly (L-Malic Acid) Production by Different Substrates Addition and Secondary Indexes in Strain Aureobasidium melanogenum

ß-poly (L-malic acid) (PMLA) is a polyester ligated by malate subunits. It has a wide prospective application as an anti-cancer drug carrier, and its malate subunits have a great application in the food industry. The strain Aureoabsidium melanogenum could produce a high amount of PMLA during fermentation, and different substrates addition could influence the production. In this study, we directly added potassium acetate, corn steep liquor, MgSO4, MnSO4, vitamin B1, vitamin B2, and nicotinamide as the fermentation substrate to the basic fermentation medium based on a generated random matrix that represented the added value. The PMLA production and four secondary indexes, pH, biomass, osmotic pressure, and viscosity were measured after 144 h fermentation. Finally, a total of 212 samples were collected as the dataset, by which the machine learning methods were deployed to predict the PMLA production by different substrates’ concentrations and the secondary indexes. The results indicated that PMLA production was negatively correlated with corn steep liquor and betaine and positively correlated with potassium acetate. The PMLA production could be predicted using all different substrates’ concentrations with a Mean Absolute Error (MAE) of 4.164 g/L and with an MAE of 6.556 g/L by different secondary indexes. Finally, the convolutional neural network (CNN) was applied to predict the PMLA production by fermentation medium images, in which the collected images were categorized into three groups, 0–20 g/L, 21–40 g/L, and >41 g/L, based on the PMLA production. The CNN model could predict the production with high accuracy. The methods and results presented in this study provided new insight into evaluating different substrates concentration on PMLA production and demonstrating the possibility of using the convolutional neural network model in the PMLA fermentation industry.

Polymalate (PMA) biosynthesis and its molecular regulation in Aureobasidium spp

It has been well documented that different strains of Aureobasidium spp. can synthesize and secrete over 30.0 g/L of polymalate (PMA) and the produced PMA has many potential applications in biomaterial, medical and food industries. The substrates for PMA biosynthesis include glucose, xylose, fructose, sucrose and glucose or fructose or xylose or sucrose-containing natural materials from industrial and agricultural wastes. Malate, the only monomer for PMA biosynthesis mainly comes from TCA cycle, cytosolic reduction TCA pathway and the glyoxylate cycle. The PMA synthetase (a NRPS) containing A like domain, T domain and C like domain is responsible for polymerization of malate into PMA molecules by formation of ester bonds between malates. PMA biosynthesis is regulated by the transcriptional activator Crz1 from Ca²⁺ signaling pathway, the GATA-type transcription factor Gat1 from nitrogen catabolite repression and the GATA-type transcription factor NsdD.

Microbial engineering for the production of C2-C6 organic acids

Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C₂-C₆ organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.

Fungi in mangrove ecosystems and their potential applications

Mangrove fungi, their ecological role in mangrove ecosystems, their bioproducts, and potential applications are reviewed in this article. Mangrove ecosystems can play an important role in beach protection, accretion promotion, and sheltering coastlines and creeks as barriers against devastating tropical storms and waves, seawater, and air pollution. The ecosystems are characterized by high average and constant temperatures, high salinity, strong winds, and anaerobic muddy soil. The mangrove ecosystems also provide the unique habitats for the colonization of fungi which can produce different kinds of enzymes for industrial uses, recycling of plants and animals in the ecosystems, and the degradation of pollutants. Many mangrove ecosystem-associated fungi also can produce exopolysaccharides, Ca²⁺-gluconic acid, polymalate, liamocin, polyunsaturated fatty acids, biofuels, xylitol, enzymes, and bioactive substances, which have many potential applications in the bioenergy, food, agricultural, and pharmaceutical industries. Therefore, mangrove ecosystems are rich bioresources for bioindustries and ecology. It is necessary to identify more mangrove fungi and genetically edit them to produce a distinct array of novel chemical entities, enzymes, and bioactive substances.

Genome sequencing of a yeast-like fungal strain P6, a novel species of Aureobasidium spp.: insights into its taxonomy, evolution, and biotechnological potentials

Purpose

This study aimed to look insights into taxonomy, evolution, and biotechnological potentials of a yeast-like fungal strain P6 isolated from a mangrove ecosystem.

Methods

The genome sequencing for the yeast-like fungal strain P6 was conducted on a Hiseq sequencing platform, and the genomic characteristics and annotations were analyzed. The central metabolism and gluconate biosynthesis pathway were studied through the genome sequence data by using the GO, KOG, and KEGG databases. The secondary metabolite potentials were also evaluated.

Results

The whole genome size of the P6 strain was 25.41Mb and the G + C content of its genome was 50.69%. Totally, 6098 protein-coding genes and 264 non-coding RNA genes were predicted. The annotation results showed that the yeast-like fungal strain P6 had complete metabolic pathways of TCA cycle, EMP pathway, pentose phosphate pathway, glyoxylic acid cycle, and other central metabolic pathways. Furthermore, the inulinase activity associated with β-fructofuranosidase and high glucose oxidase activity in this strain have been demonstrated. It was found that this yeast-like fungal strain was located at root of most species of Aureobasidium spp. and at a separate cluster of all the phylogenetic trees. The P6 strain was predicted to contain three NRPS gene clusters, five type-I PKS gene clusters, and one type-I NRPS/PKS gene cluster via analysis at the antiSMASH Website. It may synthesize epichloenin A, fusaric acid, elsinochromes, and fusaridione A.

Conclusions

Based on its unique DNA sequence, taxonomic position in the phylogenetic tree and evolutional position, the yeast-like fungal strain P6 was identified as a novel species Aureobasidium hainanensis sp. nov. P6 isolate and had highly potential applications.

Valorization of egg shell as a detoxifying and buffering agent for efficient polymalic acid production by Aureobasidium pullulans NRRL Y-2311-1 from barley straw hydrolysate

Stepwise formulation of a versatile and cost-effective medium based on barley straw hydrolysate and egg shell for efficient polymalic acid production by A. pullulans NRRL Y-2311-1 was carried out for the first time. The strain did not grow and produce polymalic acid when dilute acid pretreated barley straw hydrolysate (total fermentable sugars: 94.60 g/L; furfural: 1.01 g/L; hydroxymethylfurfural: 0.55 g/L; acetic acid: 5.06 g/L) was directly used in medium formulation without detoxification (e.g. charcoal pretreatment). When CaCO₃ in the medium formulation was substituted with egg shell powder, efficient production of polymalic acid was achieved without a detoxification step. Utilization of 40 g/L of egg shell powder led to 43.54 g polymalic acid production per L with the productivity of 0.30 g/L/h and yield of 0.48 g/g. The bioprocess strategy used in this study can also be utilized for mass production of several other industrially important microbial organic acids and biomaterials.

Production of poly(β-l-malic acid) by Aureobasidium pullulans HA-4D under solid-state fermentation

Poly(β-l-malic acid) (PMA) production by Aureobasidium pullulans HA-4D was carried out through solid-state fermentation (SSF) using agro-industrial residues. Maximum PMA production (75.4mg/g substrate) was obtained from a mixed substrate of sweet potato residue and wheat bran (1:1, w/w) supplemented with NaNO₃ (0.8%, w/w) and CaCO₃ (2%, w/w), with an initial moisture content of 70% and inoculum size of 13% (v/w) for 8days. Repeated-batch SSF was successfully conducted for 5 cycles with a high productivity. The scanning electron microscopy showed that the yeast-like cells of A. pullulans HA-4D could grow well on the solid substrate surface. Moreover, the cost analysis showed that the unit price of PMA in SSF was much lower than that of SmF. This is the first report on PMA production via SSF, and this study provided a new method to produce PMA from inexpensive agro-industrial residues.

Polymalic acid fermentation by Aureobasidium pullulans for malic acid production from soybean hull and soy molasses: Fermentation kinetics and economic analysis

Polymalic acid (PMA) production by Aureobasidium pullulans ZX-10 from soybean hull hydrolysate supplemented with corn steep liquor (CSL) gave a malic acid yield of ∼0.4g/g at a productivity of ∼0.5g/L·h. ZX-10 can also ferment soy molasses, converting all carbohydrates including the raffinose family oligosaccharides to PMA, giving a high titer (71.9g/L) and yield (0.69g/g) at a productivity of 0.29g/L·h in fed-batch fermentation under nitrogen limitation. A higher productivity of 0.64g/L·h was obtained in repeated batch fermentation with cell recycle and CSL supplementation. Cost analysis for a 5000 MT plant shows that malic acid can be produced at $1.10/kg from soy molasses, $1.37/kg from corn, and $1.74/kg from soybean hull. At the market price of $1.75/kg, malic acid production from soy molasses via PMA fermentation offers an economically competitive process for industrial production of bio-based malic acid.

Production of poly(malic acid) from sugarcane juice in fermentation by Aureobasidium pullulans: Kinetics and process economics

Poly(β-l-malic acid) (PMA) is a biodegradable polymer with many potential biomedical applications. PMA can be readily hydrolyzed to malic acid (MA), which is widely used as an acidulant in foods and pharmaceuticals. PMA production from sucrose and sugarcane juice by Aureobasidium pullulans ZX-10 was studied in shake-flasks and bioreactors, confirming that sugarcane juice can be used as an economical substrate without any pretreatment or nutrients supplementation. A high PMA titer of 116.3g/L and yield of 0.41g/g were achieved in fed-batch fermentation. A high productivity of 0.66g/L·h was achieved in repeated-batch fermentation with cell recycle. These results compared favorably with those obtained from glucose and other biomass feedstocks. A process economic analysis showed that PMA could be produced from sugarcane juice at a cost of $1.33/kg, offering a cost-competitive bio-based PMA for industrial applications.

Reconstruction of a genome-scale metabolic model and in silico analysis of the polymalic acid producer Aureobasidium pullulans CCTCC M2012223

Aureobasidium pullulans is a yeast-like fungus used for producing biopolymers e.g. polymalic acid (PMA) and pullulan. A high PMA producing strain, A. pullulans CCTCC M2012223, was isolated and sequenced in our previous study. To understand its metabolic performance, a genome-scale metabolic model, iZX637, consisting of 637 genes, 1347 reactions and 1133 metabolites, was reconstructed based on genome annotation and literature mining studies. The iZX637 model was validated by simulating cell growth, utilization of carbon and nitrogen sources, and gene essentiality analysis in A. pullulans. We further validated our model, designed a simulation program for the prediction of PMA production using experimental data, and further analyzed the carbon flux distribution and change with increasing PMA synthesis rates. Through the calculated flux distribution, NADPH- and NADH-dependent methylenetetrahydrofolate dehydrogenase (MTHFD) were found to be associated with the transfer of reducing equivalents from NADPH to NADH for supplementing NADH in the metabolic network. Furthermore, under the high PMA synthesis rate, a large amount of carbon flux was through pyruvate into malic acid via the reductive TCA cycle. Thus, pyruvate carboxylase, which can convert pyruvate to oxaloacetate with CO₂ fixation, may also be an important target for PMA synthesis. These results illustrated that the model iZX637 was a powerful tool for optimization of A. pullulans metabolism and identification of targets for guiding metabolic engineering.

Production, Purification, and Gene Cloning of a β-Fructofuranosidase with a High Inulin-hydrolyzing Activity Produced by a Novel Yeast Aureobasidium sp. P6 Isolated from a Mangrove Ecosystem

After screening of over 300 yeast strains isolated from the mangrove ecosystems, it was found that Aureobasidium sp. P6 strain had the highest inulin-hydrolyzing activity. Under the optimal conditions, this yeast strain produced an inulin-hydrolyzing activity of 30.98 ± 0.8 U/ml after 108 h of a 10-l fermentation. After the purification, a molecular weight of the enzyme which had the inulin-hydrolyzing activity was estimated to be 47.6 kDa, and the purified enzyme could actively hydrolyze both sucrose and inulin and exhibit a transfructosylating activity at 30.0 % sucrose, converting sucrose into fructooligosaccharides (FOS), indicating that the purified enzyme was a β-D-fructofuranosidase. After the full length of a β-D-fructofuranosidase gene (accession number KU308553) was cloned from Aureobasidium sp. P6 strain, a protein deduced from the cloned gene contained the conserved sequences MNDPNGL, RDP, ECP, FS, and Q of a glycosidehydrolase GH32 family, respectively, but did not contain a conserved sequence SVEVF, and the amino acid sequence of the protein from Aureobasidium sp. P6 strain had a high similarity to that of the β-fructofuranosidase from any other fungal strains. After deletion of the β-D-fructofuranosidase gene, the disruptant still had low inulin hydrolyzing and invertase activities and a trace amount of the transfructosylating activity, indicating that the gene encoding an inulinase may exist in the Aureobasidium sp. P6 strain.

Bio-products produced by marine yeasts and their potential applications

It has been well documented that the yeasts isolated from different marine environments are so versatile that they can produce various fine chemicals, enzymes, bioactive substances, single cell protein and nanoparticles. Many genes related to the biosynthesis and regulation of these functional biomolecules have been cloned, expressed and characterized. All these functional biomolecules have a variety of applications in industries of food, chemical, agricultural, biofuel, cosmetics and pharmacy. In this review, a summary will be given about these functional biomolecules and their producers of the marine yeasts as well as some related genes in order to draw an outline about necessity for further exploitation of marine yeasts and their bio-products for industrial applications.

Enhanced production of Ca²⁺-polymalate (PMA) with high molecular mass by Aureobasidium pullulans var. pullulans MCW

Background

Polymalic acid (PMA) has many applications in food and medical industries. However, so far it has not been commercially produced by fermentation. Therefore, it is very important how to develop an economical process for a large scale production of PMA by one step fermentation.

Results

After over 200 strains of Aureobasidium spp. isolated from the mangrove systems in the South of China were screened for their ability to produce Ca²⁺-polymalate (PMA), it was found that Aureobasidium pullulans var. pullulans MCW strain among them could produce high level of Ca²⁺-PMA. The medium containing only 140.0 g/L glucose, 65.0 g/L CaCO₃ and 7.5 g/L corn steep liquor was found to be the most suitable for Ca²⁺-PMA production. Then, 121.3 g/L of Ca²⁺-PMA was produced by A. pullulans var. pullulans MCW strain within 120 h at flask level. During 10-L batch fermentation, 152.52 g/L of Ca²⁺-PMA in the culture and 8.6 g/L of cell dry weight were obtained within 96 h, leaving 4.5 g/L of reducing sugar in the fermented medium. After purification of the Ca²⁺-PMA from the culture and acid hydrolysis of the purified Ca²⁺-PMA, HPLC analysis showed that A.pullulans var. pullulans MCW strain produced only one main component of Ca²⁺-PMA and the hydrolysate of the purified Ca²⁺-PMA was mainly composed of l-malic acid. Mw (the apparent molecular weight) of the purified PMA was 2.054 × 10⁵ (g/moL) and the purified PMA was estimated to be composed of 1784 l-malic acids.

Conclusions

It was found that A. pullulans var. pullulans MCW strain obtained in this study could yield 152.52 g/L of Ca²⁺-PMA within the short time, the produced PMA had the highest molecular weight and the medium for production of Ca²⁺- PMA by this yeast was very simple.

Microbial biosynthesis and secretion of l-malic acid and its applications

l-Malic acid has many uses in food, beverage, pharmaceutical, chemical and medical industries. It can be produced by one-step fermentation, enzymatic transformation of fumaric acid to l-malate and acid hydrolysis of polymalic acid. However, the process for one-step fermentation is preferred as it has many advantages over any other process. The pathways of l-malic acid biosynthesis in microorganisms are partially clear and three metabolic pathways including non-oxidative pathway, oxidative pathway and glyoxylate cycle for the production of l-malic acid from glucose have been identified. Usually, high levels of l-malate are produced under the nitrogen starvation conditions, l-malate, as a calcium salt, is secreted from microbial cells and CaCO3 can play an important role in calcium malate biosynthesis and regulation. However, it is still unclear how it is secreted into the medium. To enhance l-malate biosynthesis and secretion by microbial cells, it is very important to study the mechanisms of l-malic acid biosynthesis and secretion at enzymatic and molecular levels.