Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses

Advances in Aureobasidium research: Paving the path to industrial utilization

We here explore the potential of the fungal genus Aureobasidium as a prototype for a microbial chassis for industrial biotechnology in the context of a developing circular bioeconomy. The study emphasizes the physiological advantages of Aureobasidium, including its polyextremotolerance, broad substrate spectrum, and diverse product range, making it a promising candidate for cost-effective and sustainable industrial processes. In the second part, recent advances in genetic tool development, as well as approaches for up-scaled fermentation, are described. This review adds to the growing body of scientific literature on this remarkable fungus and reveals its potential for future use in the biotechnological industry.

Engineering the reductive tricarboxylic acid pathway in Aureobasidium pullulans for enhanced biosynthesis of poly-L-malic acid

Aureobasidium pullulans produced poly-L-malic acid (PMA) as the main metabolite in fermentation but with relatively low productivity and yield limiting its industrial application. In this study, A. pullulans ZX-10 was engineered to overexpress cytosolic malate dehydrogenase (MDH) and pyruvate carboxylase (PYC) and PMA synthetase (PMS) using a high-copy yeast episomal plasmid with the gpdA promoter from Aspergillus nidulans. Overexpressing endogenous PMS and heterologous MDH and PYC from Aspergillus oryzae respectively increased PMA production by 19 % - 37 % (0.64 - 0.74 g/g vs. 0.54 g/g for wild type) in shake-flask fermentations, demonstrating the importance of the reductive tricarboxylic acid (rTCA) pathway in PMA biosynthesis. A. pullulans co-expressing MDH and PYC produced 96.7 g/L PMA at 0.90 g/L∙h and 0.68 g/g glucose in fed-batch fermentation, which were among the highest yield and productivity reported. The engineered A. pullulans with enhanced rTCA pathway is advantageous and promising for PMA production.

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.

Recent advances in microbial production of L-malic acid

Over the last few decades, increasing concerns regarding fossil fuel depletion and excessive CO₂ emissions have led to extensive fundamental studies and industrial trials regarding microbial chemical production. As an additive or precursor, L-malic acid has been shown to exhibit distinctive properties in the food, pharmaceutical, and daily chemical industries. L-malic acid is currently mainly fabricated through a fumarate hydratase-based biocatalytic conversion route, wherein petroleum-derived fumaric acid serves as a substrate. In this review, for the first time, we comprehensively describe the methods of malic acid strain transformation, raw material utilization, malic acid separation, etc., especially recent progress and remaining challenges for industrial applications. First, we summarize the various pathways involved in L-malic acid biosynthesis using different microorganisms. We also discuss several strain engineering strategies for improving the titer, yield, and productivity of L-malic acid. We illustrate the currently available alternatives for reducing production costs and the existing strategies for optimizing the fermentation process. Finally, we summarize the present challenges and future perspectives regarding the development of microbial L-malic acid production. KEY POINTS: • A range of wild-type, mutant, laboratory-evolved, and metabolically engineered strains which could produce L-malic acid were comprehensively described. • Alternative raw materials for reducing production costs and the existing strategies for optimizing the fermentation were sufficiently summarized. • The present challenges and future perspectives regarding the development of microbial L-malic acid production were elaboratively discussed.

Metabolomics-driven strain improvement: A mini review

In recent years, mass spectrometry-based metabolomics has been established as a powerful and versatile technique for studying cellular metabolism by comprehensive analysis of metabolites in the cell. Although there are many scientific reports on the use of metabolomics for the elucidation of mechanism and physiological changes occurring in the cell, there are surprisingly very few reports on its use for the identification of rate-limiting steps in a synthetic biological system that can lead to the actual improvement of the host organism. In this mini review, we discuss different strategies for improving strain performance using metabolomics data and compare the application of metabolomics-driven strain improvement techniques in different host microorganisms. Finally, we highlight several success stories on the use of metabolomics-driven strain improvement strategies, which led to significant bioproductivity improvements.

Polymalic acid for translational nanomedicine

With rich carboxyl groups in the side chain, biodegradable polymalic acid (PMLA) is an ideal delivery platform for multifunctional purposes, including imaging diagnosis and targeting therapy. This polymeric material can be obtained via chemical synthesis, or biological production where L-malic acids are polymerized in the presence of PMLA synthetase inside a variety of microorganisms. Fermentative methods have been employed to produce PMLAs from biological sources, and analytical assessments have been established to characterize this natural biopolymer. Further functionalized, PMLA serves as a versatile carrier of pharmaceutically active molecules at nano scale. In this review, we first delineate biosynthesis of PMLA in different microorganisms and compare with its chemical synthesis. We then introduce the biodegradation mechanism PMLA, its upscaled bioproduction together with characterization. After discussing advantages and disadvantages of PMLA as a suitable delivery carrier, and strategies used to functionalize PMLA for disease diagnosis and therapy, we finally summarize the current challenges in the biomedical applications of PMLA and envisage the future role of PMLA in clinical nanomedicine.

The biosynthesis of polymalic acid (PMLA) and its biotechnical high-grade production from microorganisms compared with the chemical synthesis of PMLA

The physicochemical and biological characteristics of PMLA and its derivatives

How PMLA’s general chemical characteristics can be used to generate various macromolecular compounds for pharmaceutical delivery

The concepts of biological and clinical targeting exemplified by PMLA-based drugs and imaging agents and their biodistribution and biodegradability

An evaluation of the mechanisms that generate preclinical antitumor efficacy and the translational potential for clinical imaging

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.

Efficient poly(β-L-malic acid) production from cassava hydrolysate by cell recycle of Aureobasidium pullulans

Poly(β-L-malic acid) (PMLA) is a water-soluble, biodegradable, and biocompatible polymer with broad prospective applications and can be hydrolyzed to produce widely used acidulant L-malic acid. In order to meet an increasing demand of PMLA, we employed two effective cell-recycling strategies to produce PMLA from raw cassava hydrolysate by Aureobasidium pullulans ZD-3d. In fed-batch fermentation with raw cassava hydrolysate, 101.9 g/L PMLA was obtained with the productivity and yield of 0.77 g/L/h and 0.40 g/g, respectively. Further, three times of membrane filtration-based cell recycling fermentation was carried out, with a high productivity and yield of 1.04-1.64 g/L/h and 0.5-0.84 g/g achieved, respectively. While harnessing centrifugation-based cell recycling fermentation for five times, the productivity and yield approached 0.98-1.76 g/L/h and 0.78-0.86 g/g, respectively. To our knowledge, the processes showed the highest average PMLA productivity compared with others using low-cost biomass, which offered efficient and economical alternatives for PMLA production. KEY POINTS: • PMLA production from raw cassava hydrolysate by Aureobasidium pullulans was studied • High PMLA productivity and yield were obtained via two cell recycling strategies • The highest average PMLA productivity from low-cost biomass to date was achieved.

The signaling pathways involved in metabolic regulation and stress responses of the yeast-like fungi Aureobasidium spp

Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca²⁺ and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.

Direct conversion of cheese whey to polymalic acid by mixed culture of Aureobasidium pullulans and permeabilized Kluyveromyces marxianus

Cheese whey is an abundant and low-cost feedstock with lactose as its main component, but the inability to metabolize lactose prevents Aureobasidium pullulans from using cheese whey directly. In this study, Kluyveromyces marxianus was permeabilized to obtain nonviable but biocatalytic cells for lactose hydrolysis, and the mixed culture of A. pullulans and permeabilized K. marxianus was conducted for polymalic acid (PMA) production from cheese whey. In the mixed culture, PMA titer varied directly to β-galactosidase activity of K. marxianus, but inversely to cell viability of K. marxianus, and ethanol permeabilized K. marxianus was the most compatible with A. pullulans for PMA production. 37.8 g/L PMA was produced in batch fermentation, and PMA titer was increased to 97.3 g/L in fed-batch fermentation, with a productivity of 0.51 g/(L·h) and a yield of 0.56 g/g. This study paved an economical and environmentally friendly way for PMA production from cheese whey.

Coproduction of polymalic acid and liamocins from two waste by-products from the xylitol and gluconate industries by Aureobasidium pullulans

The coproduction of polymalic acid (PMA) and liamocins, two important metabolites secreted by Aureobasidium pullulans, from two waste by-products from the xylitol and gluconate industries was investigated in shake flasks and fermentors, confirming that waste xylose mother liquor (WXML) could be utilized as an economical feedstock without any pretreatment. Gluconate could strengthen carbon flux and NADPH supply for the synergetic biosynthesis of PMA and liamocins. High PMA and liamocin titers of 82.9 ± 2.1 and 28.3 ± 2.7 g/L, respectively, were obtained from the coupled WXML and waste gluconate mother liquor (WGML) in batch fermentation, with yields of 0.84 and 0.25 g/g, respectively. These results are comparable to those obtained from renewable feedstocks. Economic assessment of the process revealed that PMA and liamocins could be coproduced from two by-products at costs of $1.48/kg or $0.67/kg (with liamocins credit), offering an economic and sustainable process for the application of waste by-products.

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.

Sustainable production and biomedical application of polymalic acid from renewable biomass and food processing wastes

Polymalic acid (PMA), a homopolymer of L-malic acid (MA) generated from a yeast-like fungus Aureobasidium pullulans, has unique properties and many applications in food, biomedical, and environmental fields. Acid hydrolysis of PMA, releasing the monomer MA, has become a novel process for the production of bio-based MA, which currently is produced by chemical synthesis using petroleum-derived feedstocks. Recently, current researches attempted to develop economically competitive process for PMA and MA production from renewable biomass feedstocks. Compared to lignocellulosic biomass, PMA and MA production from low-value food processing wastes or by-products, generated from corn, sugarcane, or soybean refinery industries, showed more economical and sustainable for developing a MA derivatives platform from biomass biorefinery to chemical conversion. In the review, we compared the process feasibility for PMA fermentation with lignocellulosic biomass and food process wastes. Some useful strategies for metabolic engineering are summarized. Its changeable applicability and future prospects in food and biomedical fields are also discussed.

Biosynthetic Polymalic Acid as a Delivery Nanoplatform for Translational Cancer Medicine

Poly(β-L-malic acid) (PMLA) is a natural polyester produced by numerous microorganisms. Regarding its biosynthetic machinery, a nonribosomal peptide synthetase (NRPS) is proposed to direct polymerization of L-malic acid in vivo. Chemically versatile and biologically compatible, PMLA can be used as an ideal carrier for several molecules, including nucleotides, proteins, chemotherapeutic drugs, and imaging agents, and can deliver multimodal theranostics through biological barriers such as the blood–brain barrier. We focus on PMLA biosynthesis in microorganisms, summarize the physicochemical and physiochemical characteristics of PMLA as a naturally derived polymeric delivery platform at nanoscale, and highlight the attachment of functional groups to enhance cancer detection and treatment.

CRISPR/Cas9-mediated efficient genome editing via protoplast-based transformation in yeast-like fungus Aureobasidium pullulans

Aureobasidium pullulans, a yeast-like fungus with strong environmental adaptability, remains a potential host for bio-production of different valuable metabolites. However, its potential application is limited by low-efficient genetic manipulation. In this study, CRISPR/Cas9-mediated genome editing via protoplast-based transformation system was developed. To test CRISPR/Cas9 mediated genomic mutagenesis, the orotidine 5-phosphate decarboxylase (umps) gene was used as a counter-selectable selection marker. By co-transforming of two plasmids harboring cas9 gene and a guide RNA targeting umps, respectively, the CRISPR/Cas9 system could significantly increase frequency of mutation in the targeting site of guide RNA. To further validate that CRISPR/Cas9 stimulated homologous recombination with donor DNA, a color reporter system of beta-glucuronidase (gus) gene was developed for calculating positive mutation rate. The results showed that positive mutation rate with CRISPR/Cas9 system was ~40% significantly higher than only with the donor DNA (~4%). Furthermore, the different posttranscriptional RNA processing schemes were analyzed by compared the effects of flanking gRNA with self-cleaving ribozymes or tRNA. The result demonstrated that gRNA processed by self-cleaving ribozymes achieves higher positive mutant rate. This study provided foundation for a simple and powerful genome editing tool for A. pullulans. Moreover, a counter-selectable selection marker (umps) and a color reporter system (gus) were being developed as genetic parts for strain engineering.

The Multiple and Versatile Roles of Aureobasidium pullulans in the Vitivinicultural Sector

The saprophytic yeast-like fungus Aureobasidium pullulans has been well documented for over 60 years in the microbiological literature. It is ubiquitous in distribution, being found in a variety of environments (plant surfaces, soil, water, rock surfaces and manmade surfaces), and with a worldwide distribution from cold to warm climates and wet/humid regions to arid ones. Isolates and strains of A. pullulans produce a wide range of natural products well documented in the international literature and which have been regarded as safe for biotechnological and environmental applications. Showing antagonistic activity against plant pathogens (especially post-harvest pathogens) is one of the major applications currently in agriculture of the fungus, with nutrient and space competition, production of volatile organic compounds, and production of hydrolytic enzymes and antimicrobial compounds (antibacterial and antifungal). The fungus also shows a positive role on mycotoxin biocontrol through various modes, with the most striking being that of binding and/or absorption. A. pullulans strains have been reported to produce very useful industrial enzymes, such as β-glucosidase, amylases, cellulases, lipases, proteases, xylanases and mannanases. Pullulan (poly-α-1,6-maltotriose biopolymer) is an A. pullulans trademark product with significant properties and biotechnological applications in the food, cosmetic and pharmaceutical industries. Poly (β-l-malic acid), or PMA, which is a natural biopolyester, and liamocins, a group of produced heavy oils and siderophores, are among other valuable compounds detected that are of possible biotechnological use. The fungus also shows a potential single-cell protein source capacity with high levels of nucleic acid components and essential amino acids, but this remains to be further explored. Last but not least, the fungus has shown very good biocontrol against aerial plant pathogens. All these properties are of major interest in the vitivinicultural sector and are thoroughly reviewed under this prism, concluding on the importance that A. pullulans may have if used at both vineyard and winery levels. This extensive array of properties provides excellent tools for the viticulturist/farmer as well as for the oenologist to combat problems in the field and create a high-quality wine.