Highlights
- •Aureobasidium spp. can produce much more extracellular enzymes and natural products than any other fungi.
- •They have rich sources of regulatory elements.
- •Genome editing techniques for them are available.
- •Aureobasidium spp. are the ideal chassises for fungal biotechnology and biology.
Abstract
Aureobasidium spp. are the dimorphic fungi which have both major yeast cells and minor filamentous cells. Different strains of Aureobasidium spp. can synthesize different enzymes for utilization of a wide range of substrates including various wastes. Aureobasidium spp. also can synthesize many natural products such as pullulan, β-glucan, polymalate, liamocins, siderophores and melanin which have many applications in various sectors of biotechnology. Furthermore, their synthetic pathways, the relevant enzymes and their encoding genes have been clearly elucidated. Meanwhile, the genomes of over 70 different strains of Aureobasidium spp. have been sequenced and functionally annotated. The genomic DNAs of some strains of Aureobasidium spp. are wholly duplicated and such whole genome duplicated strains are polyextremotolerant. Different genetic vectors for efficiently editing genomic DNAs and natural products of Aureobasidium spp. are available. They have plenty of structural and regulatory elements controlling and regulating synthesis of many natural products and enzymes. Importantly, pullulan produced by different strains of Aureobasidium spp. has been commercially produced world-wide for a long time. Therefore, like Aspergillus spp., Penicillium spp., and Saccharomyces cerevisiae, Aureobasidium spp. will be the emerging eucaryotic cells for fungal biotechnology and biology.
Introduction
Aureobasidium spp. are the dimorphic fungi which have both major yeast cells and minor filamentous cells. Because most strains of the yeast-like fungi can synthesize melanin and accumulate it in their cell walls, Aureobasidium spp. are also called black yeasts [1]. Aureobasidium spp. are well known due to the facts that they have ability to synthesize and secret high level of pullulan into medium [1]. In facts, Aureobasidium spp. have an ability to synthesize and secrete high level of liamocin, polymalate, siderophore, fumaric acid, β-glycan, Aureobasidin A and other natural products, too. It has been reported that Aureobasidium spp. also can secrete glucose oxidase to catalyze glucose into gluconic acid [2], β-fructofuranosidase to transform sucrose into fructooligosaccharides [3] and any other high activity enzymes.
In recent years, many new species and varieties of the genus have been identified. They include Aureobasidium lini, Aureobasidium proteae, Aureobasidium microstictum, Aureobasidium pullulans, Aureobasidium subglaciale, Aureobasidium namibiae, Aureobasidium melanogenum, Aureobasidium pullulans var. aubasidan, Aureobasidium caulivorum, Aureobasidium leucospermi, Aureobasidium iranianum, Aureobasdium mangrovei, Aureobasidium thailandense, Aureobasidium pini, Aureobasidium khasianum, Aureobasidium hainanensis, Aureobasidium mustum, Aureobasidium vineae and Aureobasidium uvarum [4], [5], [6], [7], [8]. As more strains of Aureobasidium spp. are isolated and identified, more new species will be found [6], [7], [8]. Among them, A. melanogenum is the most frequently isolated species and is widely distributed in various environments, followed by A. pullulans [5]. Meanwhile, most of the discovered natural products are produced by A. melanogenum, A. pullulans, A. hainanensis sp. nov. P6 and A. pullulans var. aubasidani [6], [7], [8], [9]. However, more natural products from any other strains of Aureobasidium spp. cultivated under different conditions are needed to be further mined. It has been well confirmed that they have poly-extremotolerant–the ability to resist different environmental stresses and to have a wide range of enzymatic profiles for utilization of various natural substrates [10]. So, Aureobasidium spp. are widely distributed in various surroundings such as desert, mangrove ecosystem, saltern ponds, natural honey, deep sea, Antarctica, glacial ice and so on, meaning that they can be adapted to various environments [10], [11], [12], [13], [14], [15], [16]. Sometimes, high osmotic pressure (high concentration of sugar and salts), low and high pHs, high and low temperatures, low nitrogen concentration (nitrogen starvation) also occur during cultivation and fermentation of a fungus. Therefore, it is very important for the fungal cells to have such poly-extremotolerant properties.
Furthermore, the genomic DNAs of many strains of the genus have been sequenced and functionally annotated and the genomic editing techniques for their genomes and natural products have been established [5], [6], [7], [8], [17], [18], [19].
In recent years, it has been well evidenced that Aureobasidium spp. can be the excellent fungal cells for fungal synthetic biology and metabolic engineering because different strains of Aureobasidium spp. have high ability to synthesize many natural products from different substrates and have various enzyme secretion capacity for utilization of various natural polymers and monomers [6], [20], [21], [22], [23]. It is easy to make their growth to high cell densities [3]; They are suitable for industrial use as cell factories [24]. Their genomes and chemical structures of natural products such as pullulan and liamocins can be easily edited at molecular levels and many selectable markers have been available, leading to their proficient DNA recombination [19], [25]; Aureobasidium spp. have a lack of susceptibility to bacteriophage and can withstand various stress conditions as mentioned above [26]. In recent years, extensive existing research on Aureobasidium spp. [23], [25], [27], [28], [29], [30] has been done in many laboratories in this world.
It has been well known that Aspergillus spp. are predominantly used for food fermentation and large-scale production of enzymes such as glucoamylase, organic acids such as citric acid, and bioactive compounds [31] while Penicillium spp. are being used for a large-scale production of penicillin [32] and Trichoderma spp. can produce high activity of cellulase [33]. Although the filamentous fungal cells, especially Aspergillus spp. Penicillium spp. and Trichoderma spp. also share some of these advantageous characteristics with Aureobasidium spp., they are often more difficult to be genetically operated with foreign or homologous DNAs and to be cultivated in a large-scale fermenter than Aureobasidium spp. [34]. This is due to the large-scale growth of the filamentous fungi with hyphal morphology that can easily lead to mixing difficulties, oxygen and mass transfer limitations [35] while as mentioned above, most of the cells of Aureobasidium spp. in the medium are yeast-like cells, not filamentous cells [1]. Furthermore, the native strains of Aspergillus spp. Penicillium spp. and Trichoderma spp. have no ability to synthesize some products, such as pullulan, polymalate, liamocins and fumaric acid. However, Aureobasidium spp. have such an ability. Meanwhile, S. cerevisiae has been used by human for a large scale of ethanol and single cell protein production for millennia in food, wine and biofuel production industries [36], [37]. As a unique unicellular fungal cell, it has a dominating position in basic research on eucaryotic organisms, synthetic biology, fungal biology and biotechnology. It is a widely employed and mostly used single eucaryotic cell in the field of biotechnology and basic biology research due to its well-annotated genome, well-known physiology and clear genetic background as well as easy cultivation and genetic transformation. Although as a good fungal single cell, cell factory and the model yeast strain, S. cerevisiae also has been widely used in eucaryotic synthetic biology, the native enzymes and natural products produced by it and the natural substrates it can utilize are very limited [38]. For example, S. cerevisiae cannot synthesize cellulase, xylanase, inulinase, pullulan, polymalate, liamocins, siderophore, is deficient in xylose utilization and so on. In order to reduce ethanol production and increase other product production in an engineered strain, six NADH-dependent alcohol dehydrogenase isozymes encoded by the adh1, adh2, adh3, adh4, adh5, and sfa1 genes in S. cerevisiae must be deleted [38]. In order to produce ethanol from starch, cellulose, inulin, and xylose, many genes encoding α-amylase, glucoamylase, cellulases, inulinase, xylose isomerase, xylose dehydrogenase so on must be overexpressed in S. cerevisiae. In order to enhance its ethanol tolerance and thermotolerance, many genes must also be introduced. So, there are also many potential advantages of Aureobasidium spp. over S. cerevisiae and any other fungi for developing a new cell factory for fungal biotechnology, synthetic biology and biochemistry. Aureobasidium spp. are the fantastic yeast-like fungi with the unique characteristics of metabolisms and physiology as well as many applications in biotechnology. This review article is mainly focused on the full summary on recent progress in physiology, synthetic pathways, genetics and applications of Aureobasidium spp.
Section snippets
Aureobasidium spp. have all kinds of extracellular enzymes for utilizing a wide range of substrates
In order to produce biochemicals and greatly reduce production costs, it is very important for a cell factory to utilize a wide range of substrates, especially, starch, sucrose, molasses, glucose, fructose, xylose, cellulose, xylan and sucrose, cellulose, xylan, xylose and inulin-containing raw materials, industrial and agricultural wastes which are cheap materials and available in every corner of the world. Different strains of Aureobasidium spp. isolated from different environments can
Pullulan
It has well documented that pullulan produced by different strains of Aureobasidium spp. has wide applications in food, pharmaceutical, chemical, environmental and cosmetic industries [27], [62]. High level of pullulan is synthesized by different strains of Aureobasidium spp. only when they are grown in the medium containing high ratio of carbon (glucose or sucrose) to nitrogen [27]. The produced pullulan has crucial roles in resistance of the producers to the stressed environments, such as UV
Genomic DNAs of many Aureobasidium spp. have been sequenced and the genome editing tools are available
To date, the genomic DNAs of many strains of Aureobasidium spp. [2], [5], [7], [10], [39], [56], [59], [135], [136] have been sequenced and functionally annotated. After the genomes of 50 strains of A. pullulans from different habitats and geographic locations were sequenced and analyzed, it was found that the mean genome size, GC content and gene numbers were 28. 04 Mb, 50.65% and 10646, respectively [10]. In this case, all the genes responsible for the structural genes, their promoters,
Aureobasidium spp. have rich sources of regulatory elements
Transcriptional regulatory elements can be divided into transcriptional activators and transcriptional repressors. The transcriptional activators and transcriptional repressors are also catalogued into general transcriptional factors and specific transcriptional factors, respectively. They can play very important roles in regulation of primary and secondary metabolisms in organisms. For example, they can increase production of useful metabolites, decrease synthesis of harmful products, aid in
Aureobasidium spp. can be easily applied to fermentation industries
Pullulan is the most popular fermentation product produced by different strains of Aureobasidium spp. and has been broadly used in different sectors in biotechnology for over forty years. The commercial production of pullulan began in 1976 by the Hayashibara Company in Japan and pullulan films were commercialized by Hayashibara Company in 1982 [139]. As mentioned above, the pullulan level synthesized by A. melanogenum TN3–1 isolated from the natural honey and grown in the medium containing
Conclusion and future perspectives
All the results above demonstrate that Aureobasidium spp. are an ideal fungal cell for fungal biology, fungal biotechnology, metabolic engineering and synthetic biology compared to any other fungi, such as S. cerevisiae because their genomes can be easily edited. As the cell factory, Aureobasidium spp. can be easily applied to fermentation industries because they have all kinds of extracellular enzymes for utilizing a wide range of substrates and have rich resources of natural products with
Ethical approval
Not required.
CRediT authorship contribution statement
PW and SLJ conducted and collected all the data for the Figure and Tables. ZC and GLL analyzed data. ZMC wrote the manuscript. All authors read and approved the manuscript.
Declaration of Competing Interest
The authors declare that there are no competing interests associated with the manuscript.
Acknowledgements
The research work was supported by the research grants from National Natural Science Foundation of China (Grant Nos. 31500029 and 31970058). The research work was also supported by research grants (Nos. 202066002 and 2021BC009) from the Fundamental Research Funds for the Central Universities and from Bingtuan Science and Technology Program of China.
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