Assessment of Schwanniomyces occidentalis as a host for protein production using the wide-range Xplor2 expression platform

Toolbox for Genetic Transformation of Non-Conventional Saccharomycotina Yeasts: High Efficiency Transformation of Yeasts Belonging to the Schwanniomyces Genus

Non-conventional yeasts are increasingly being investigated and used as producers in biotechnological processes which often offer advantages in comparison to traditional and well-established systems. Most biotechnologically interesting non-conventional yeasts belong to the Saccharomycotina subphylum, including those already in use (Pichia pastoris, Yarrowia lypolitica, etc.), as well as those that are promising but as yet insufficiently characterized. Moreover, for many of these yeasts the basic tools of genetic engineering needed for strain construction, including a procedure for efficient genetic transformation, heterologous protein expression and precise genetic modification, are lacking. The first aim of this study was to construct a set of integrative and replicative plasmids which can be used in various yeasts across the Saccharomycotina subphylum. Additionally, we demonstrate here that the electroporation procedure we developed earlier for transformation of B. bruxellensis can be applied in various yeasts which, together with the constructed plasmids, makes a solid starting point when approaching a transformation of yeasts form the Saccharomycotina subphylum. To provide a proof of principle, we successfully transformed three species from the Schwanniomyces genus (S. polymorphus var. polymorphus, S. polymorphus var. africanus and S. pseudopolymorphus) with high efficiencies (up to 8 × 10³ in case of illegitimate integration of non-homologous linear DNA and up to 4.7 × 10⁵ in case of replicative plasmid). For the latter two species this is the first reported genetic transformation. Moreover, we found that a plasmid carrying replication origin from Scheffersomyces stipitis can be used as a replicative plasmid for these three Schwanniomyces species.

Development of a Vector Set for High or Inducible Gene Expression and Protein Secretion in the Yeast Genus Blastobotrys

Converting lignocellulosic biomass into value-added products is one of the challenges in developing a sustainable economy. Attempts to engineer fermenting yeasts to recover plant waste are underway. Although intensive metabolic engineering has been conducted to obtain Saccharomyces cerevisiae strains capable of metabolising pentose sugars mainly found in hemicellulose, enzymatic hydrolysis after pretreatment is still required. Blastobotrys raffinosifermentans, which naturally assimilates xylose and arabinose and displays numerous glycoside hydrolases, is a good candidate for direct and efficient conversion of renewable biomass. However, a greater diversity of tools for genetic engineering is needed. Here, we report the characterisation of four new promising promoters, a new dominant marker, and two vectors for the secretion of epitope tagged proteins along with a straightforward transformation protocol. The TDH3 promoter is a constitutive promoter stronger than TEF1, and whose activity is maintained at high temperature or in the presence of ethanol. The regulated promoters respond to high temperature for HSP26, gluconeogenic sources for PCK1 or presence of xylose oligomers for XYL1. Two expression/secretion vectors were designed based on pTEF1 and pTDH3, two endogenous signal peptides from an α-arabinanase and an α-glucuronidase, and two epitopes. A heterologous α-arabinoxylan hydrolase from Apiotrichum siamense was efficiently secreted using these two vectors.

Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production

Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.

Selection of the Optimal Yeast Host for the Synthesis of Recombinant Enzymes

Yeasts, like Arxula adeninivorans, Hansenula polymorpha, Pichia pastoris, Debaryomyces hansenii, Debaryomyces polymorphus, Schwanniomyces occidentalis, Yarrowia lipolytica, and Saccharomyces cerevisiae are frequently used producers of recombinant enzymes, particularly when posttranslational modifications are mandatory to obtain full functionality. The wide-range transformation/expression platform presented in this chapter can be used to select the optimal yeast host for high-level synthesis of the desired enzyme with favorable biochemical properties. This platform is composed of a selection marker and up to four expression modules in a linearized cassette. Here we describe the protocols for the assembly as well as the transformation of yeast strains with the respective cassettes, screening of transformants, the isolation and biochemical characterization of the enzymes, and finally a simple fermentation strategy to achieve maximal yields of the chosen recombinant enzyme.

Established and Upcoming Yeast Expression Systems

Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.

Production of (R)-3-hydroxybutyric acid by Arxula adeninivorans

(R)-3-hydroxybutyric acid can be used in industrial and health applications. The synthesis pathway comprises two enzymes, β-ketothiolase and acetoacetyl-CoA reductase which convert cytoplasmic acetyl-CoA to (R)-3-hydroxybutyric acid [(R)-3-HB] which is released into the culture medium. In the present study we used the non-conventional yeast, Arxula adeninivorans, for the synthesis enantiopure (R)-3-HB. To establish optimal production, we investigated three different endogenous yeast thiolases (Akat1p, Akat2p, Akat4p) and three bacterial thiolases (atoBp, thlp, phaAp) in combination with an enantiospecific reductase (phaBp) from Cupriavidus necator H16 and endogenous yeast reductases (Atpk2p, Afox2p). We found that Arxula is able to release (R)-3-HB used an existing secretion system negating the need to engineer membrane transport. Overexpression of thl and phaB genes in organisms cultured in a shaking flask resulted in 4.84 g L⁻¹ (R)-3-HB, at a rate of 0.023 g L⁻¹ h⁻¹ over 214 h. Fed-batch culturing with glucose as a carbon source did not improve the yield, but a similar level was reached with a shorter incubation period [3.78 g L⁻¹ of (R)-3-HB at 89 h] and the rate of production was doubled to 0.043 g L⁻¹ h⁻¹ which is higher than any levels in yeast reported to date. The secreted (R)-3-HB was 99.9% pure. This is the first evidence of enantiopure (R)-3-HB synthesis using yeast as a production host and glucose as a carbon source.

Enhancement of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) accumulation in Arxula adeninivorans by stabilization of production

Background

In recent years the production of biobased biodegradable plastics has been of interest of researchers partly due to the accumulation of non-biodegradable plastics in the environment and to the opportunity for new applications. Commonly investigated are the polyhydroxyalkanoates (PHAs) poly(hydroxybutyrate) and poly(hydroxybutyrate-co-hydroxyvalerate) (PHB-V). The latter has the advantage of being tougher and less brittle. The production of these polymers in bacteria is well established but production in yeast may have some advantages, e.g. the ability to use a broad spectrum of industrial by-products as a carbon sources.

Results

In this study we increased the synthesis of PHB-V in the non-conventional yeast Arxula adeninivorans by stabilization of polymer accumulation via genetic modification and optimization of culture conditions. An A. adeninivorans strain with overexpressed PHA pathway genes for β-ketothiolase, acetoacetyl-CoA reductase, PHAs synthase and the phasin gene was able to accumulate an unexpectedly high level of polymer. It was found that an optimized strain cultivated in a shaking incubator is able to produce up to 52.1% of the DCW of PHB-V (10.8 g L⁻¹) with 12.3%mol of PHV fraction. Although further optimization of cultivation conditions in a fed-batch bioreactor led to lower polymer content (15.3% of the DCW of PHB-V), the PHV fraction and total polymer level increased to 23.1%mol and 11.6 g L⁻¹ respectively. Additionally, analysis of the product revealed that the polymer has a very low average molecular mass and unexpected melting and glass transition temperatures.

Conclusions

This study indicates a potential of use for the non-conventional yeast, A. adeninivorans, as an efficient producer of polyhydroxyalkanoates.

Blastobotrys (Arxula) adeninivorans: a promising alternative yeast for biotechnology and basic research

Blastobotrys adeninivorans (syn. Arxula adeninivorans) is a non-conventional, non-pathogenic, imperfect, haploid yeast, belonging to the subphylum Saccharomycotina, which has to date received comparatively little attention from researchers. It possesses unusual properties such as thermo- and osmotolerance, and a broad substrate spectrum. Depending on the cultivation temperature B. (A.) adeninivorans exhibits different morphological forms and various post-translational modifications and protein expression properties that are strongly correlated with the morphology. The genome has been completely sequenced and, in addition, there is a well-developed transformation/expression platform, which makes rapid, simple gene manipulations possible. This yeast species is a very good host for homologous and heterologous gene expression and is also a useful gene donor. Blastobotrys (A.) adeninivorans is able to use a very wide range of substrates as carbon and/or nitrogen sources and is an interesting organism owing to the presence of many metabolic pathways, for example degradation of n-butanol, purines and tannin. In addition, its unusual properties and robustness make it a useful bio-component for whole cell biosensors. There are currently a number of products on the market produced by B. (A.) adeninivorans and further investigation may contribute further innovative solutions for current challenges that exist in the biotechnology industry. Additionally it may become a useful alternative to existing commercial yeast strains and as a model organism in research. In this review we present information relevant to the exploitation of B. (A.) adeninivorans in research and industrial settings. Copyright © 2016 John Wiley & Sons, Ltd.

Selection of oleaginous yeasts for fatty acid production

Background

Oleaginous yeast species are an alternative for the production of lipids or triacylglycerides (TAGs). These yeasts are usually non-pathogenic and able to store TAGs ranging from 20 % to 70 % of their cell mass depending on culture conditions. TAGs originating from oleaginous yeasts can be used as the so-called second generation biofuels, which are based on non-food competing “waste carbon sources”.

Results

In this study the selection of potentially new interesting oleaginous yeast strains is described. Important selection criteria were: a broad maximum temperature and pH range for growth (robustness of the strain), a broad spectrum of carbon sources that can be metabolized (preferably including C-5 sugars), a high total fatty acid content in combination with a low glycogen content and genetic accessibility.

Conclusions

Based on these selection criteria, among 24 screened species, Schwanniomyces occidentalis (Debaromyces occidentalis) CBS2864 was selected as a promising strain for the production of high amounts of lipids.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0276-7) contains supplementary material, which is available to authorized users.

Purification and immunodetection of the complete recombinant HER-2[neu] receptor produced in yeast

For the first time, the full length recombinant HER-2[neu] receptor has been produced in a yeast (Arxula adeninivorans). It is one of the most studied membrane receptors in oncology and is involved in aggressive tumor formation. A yeast integration rDNA cassette containing the human gene coding for the HER-2[neu] protein was constructed and a screening procedure was performed to select the most productive transformant. Different detergents were tested for efficient solubilization of the membrane bound protein, with CHAPS giving the best results. To increase the yield of the recombinant protein from HER-2[neu] producing A. adeninivorans, optimal culture parameters were established for cultivation in bioreactor. The recombinant protein was subsequently assayed using ELISA and SPR immunoassays systems with antibodies raised against two different epitopes of the human receptor. In both cases, elution fractions containing the recombinant HER-2[neu] receptor successfully reacted with the immunoassays with limits of quantification below 100ngml(-1). These results demonstrate that the full length recombinant HER-2[neu] reported here has the potential to be a new standard for the detection of HER-2 type cancer.