Analysis of glucose and xylose metabolism in new indigenous Meyerozyma caribbica strains isolated from corn residues

Aiming to broaden the base of knowledge about wild yeasts, four new indigenous strains were isolated from corn residues, and phylogenetic-tree assemblings on ITS and LSU regions indicated they belong to Meyerozyma caribbica. Yeasts were cultivated under full- and micro-aerobiosis, starting with low or high cell-density inoculum, in synthetic medium or corn hydrolysate containing glucose and/or xylose. Cells were able to assimilate both monosaccharides, albeit by different metabolic routes (fermentative or respiratory). They grew faster in glucose, with lag phases ~ 10 h shorter than in xylose. The hexose exhaustion occurred between 24 and 34 h, while xylose was entirely consumed in the last few hours of cultivation (44-48 h). In batch fermentation in synthetic medium with high cell density, under full-aerobiosis, 18-20 g glucose l^-1 were exhausted in 4-6 h, with a production of 6.5-7.0 g ethanol l^-1. In the xylose medium, cells needed > 12 h to consume the carbohydrate, and instead of ethanol, cells released 4.4-6.4 g l^-1 xylitol. Under micro-aerobiosis, yeasts were unable to assimilate xylose, and glucose was more slowly consumed, although the ethanol yield was the theoretical maximum. When inoculated into the hydrolysate, cells needed 4-6 h to deplete glucose, and xylose had a maximum consumption of 57%. Considering that the hydrolysate contained ~ 3 g l^-1 acetic acid, it probably has impaired sugar metabolism. Thus, this study increases the fund of knowledge regarding indigenous yeasts and reveals the biotechnological potential of these strains.

Detecting the Non-conventional mRNA Splicing and Translational Activation of HAC1 in Budding Yeast

Protein-folding homeostasis in the endoplasmic reticulum (ER) is maintained by the unfolded protein response (UPR). UPR in Saccharomyces cerevisiae is regulated by a bZIP transcription factor, Hac1p. Under non-stress condition, HAC1 mRNA is translationally repressed. When un- or mis-folded proteins accumulate in the ER, HAC1 mRNA undergoes non-conventional mRNA splicing. The spliced HAC1 mRNA is translationally active and produces functional Hac1p, which initiates a transcriptional response that restores ER protein-folding homeostasis. Thus, the activation of yeast UPR is tightly regulated by HAC1 mRNA splicing. Here, we describe two methods that are used to monitor the splicing and translational status of HAC1 mRNA in budding yeast.

Investigating Fungal Biosynthetic Pathways Using Pichia pastoris as a Heterologous Host

Fungal natural products have extensive biological activities, and thus have been largely commercialized in the pharmaceutical, agricultural, and food industries. Recently, heterologous expression has become an irreplaceable technique to functionalize fungal biosynthetic gene clusters and synthesize fungal natural products in various chassis organisms. This chapter describes the general method of using Pichia pastoris as a chassis host to investigate fungal biosynthetic pathways.

Staining of the Actin Cytoskeleton During Cell Division in Budding Yeast and Mammalian Cells

Observation of actin at the cortex in dividing cells can be accomplished using the fungal toxin phalloidin conjugated to fluorophores. Protocols for staining both budding yeast and cultured mammalian cells with fluorescent phalloidin are described. This technique can be combined with immunofluorescence to image actin filaments and other proteins involved in cell division simultaneously.

Production of Single-Domain Antibodies in Pichia pastoris

Single-domain antibodies (sdAbs) are binders that consist of a single immunoglobulin domain. SdAbs have gained importance as therapeutics, diagnostic reagents, and research tools. Functional sdAbs are commonly produced in Escherichia coli, which is a simple and widely used host for production of recombinant proteins. However, there are drawbacks of the E. coli expression system, including the potential for misfolded recombinant proteins and pyrogenic contamination with toxic lipopolysaccharides. Pichia pastoris is an alternative host for the production of heterologous proteins because of its high recombinant protein yields and the ability to produce soluble, properly folded proteins without lipopolysaccharide contamination. Here, we describe a method to produce sdAbs in P. pastoris. We present methods for the cloning of sdAb-encoding genes into a P. pastoris expression vector, production and purification of sdAbs, and measurement of sdAb-binding kinetics. Functional sdAbs are easily and routinely obtained using these methods.

DNA-RNA Hybrids at Telomeres in Budding Yeast

It has recently been demonstrated that budding yeast telomeres are transcribed into TERRA, a long noncoding RNA. Due to the G-rich nature of the coding strand, TERRA has a tendency to form DNA-RNA hybrids and potentially R-loops, which in turn, promote repair at short telomeres. Here, we report two methods to detect DNA-RNA hybrids at yeast telomeres, namely, DRIP, which employs the S9.6 hybrid-recognizing antibody, and R-ChIP, which takes advantage of a catalytic dead form of RNase H1 (Rnh1-cd). We use cross-linked material for both protocols as we have found that this does not negatively affect recovered material, and furthermore allows the precipitation of other proteins from the identical cross-linked material. Although both methods are successful in terms of detecting DNA-RNA hybrids at telomeres, the R-ChIP method yields an approximately ten-fold increased enrichment.

A Method for Production of Human Adenosine Deaminase 1 (ADA1) in Pichia pastoris Provides Needed Quality Control Material for Clinical Laboratories

OBJECTIVE

Adenosine deaminase (ADA) plays a major role in maintaining metabolic homeostasis via catalysis of hydrolytic deamination of adenosine to inosine. The ADA1 isoenzyme of ADA is an analyte tested in clinical laboratories; however, lack of quality control (QC) material in terms of enzyme homogeneity, stability, and coverage of the clinically relevant analytical measurement range (AMR), poses a challenge for adequate monitoring of this analyte. The aim of this study was to address the need for manufacture of QC material through recombinant expression of catalytically active ADA1 in eukaryotic cells (Pichia pastoris GS115).

METHODS

The coding region of ADA1 gene was amplified by PCR and ligated into plasmid pPICZαA, followed by transfer into P. pastoris using electroporation. Recombinant ADA1 produced by P. pastoris was purified using a Ni-NTA resin column, yielding 5 mL of purified ADA1 with an activity of 4200.6 U/L. Purified ADA1 protein was added to human donor serum as the appropriate matrix for QC materials preparation.

RESULTS

One hundred vials of lyophilized ADA1 were prepared at clinically significant concentrations at 41.6 U/L and 115.5 U/L (50 vials each). Both concentrations were homogenous and stable at room temperature (RT, 22-24°C) for at least 7 d, at 4°C for 3 months, and at -20°C for 12 months. Reconstituted aliquots of QC material were found to be stable at -20°C for up to 60 d and should be used within 8 h or 48 h when stored at RT or 4°C, respectively.

CONCLUSION

Success of this ADA1 expression system presents a potential solution to increase production options available to clinical laboratories.

Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN

Genome-scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms. While the applications of GEMs are wide and far reaching, the reconstruction and continuous curation of such models can be perceived as a tedious and time-consuming task. Using RAVEN, a MATLAB-based toolbox designed to facilitate the reconstruction analysis of metabolic networks, this protocol practically demonstrates how researchers can create their own GEMs using a homology-based approach. To provide a complete example, a draft GEM for the industrially relevant yeast Hansenula polymorpha is reconstructed.

Expression of Recombinant Rat Secretable FNDC5 in Pichia Pastoris and Detection of Its Biological Activity

FNDC5 is the precursor of the myokine irisin proposed to exhibit favorable metabolic activity, including anti-obesity and anti-diabetes effects. The diversity of FNDC5 transcripts has been reported by several studies, but the role and existence of these transcripts are not well defined. In our previous study, a novel secretable FNDC5 (sFNDC5) isoform lacking the transmembrane region was found in rat INS-1 cells and multiple rat tissues. In the current study, we established a high-yield system for the expression and purification of sFNDC5 in Pichia pastoris, and functional investigations were undertaken using 3T3-L1 cells. We discovered that this new isoform has similar and even stronger biological functions than irisin, which may be due to its more complete structure without cleavage. Hence, we believe that sFNDC5, as the first identified readily secretable derivative, can better induce lipolysis and can potentially prevent obesity and related metabolic diseases.

Sucrose gradient chromatin enrichment for quantitative proteomics analysis in budding yeast

Here, we describe a fractionation protocol optimized to quantify changes in relative abundance of the chromatin-bound proteome (chromatome) by tandem mass tag multiplexing-based tandem mass spectrometry. It has been applied to yeast cells before and after exposure to DNA-damaging drugs to characterize changes in chromatin composition induced by the DNA damage response. We detail steps for stringent chromatin fractionation, sample preparation for mass spectrometry, and its evaluation. For complete details on the use and execution of this protocol, please refer to Challa et al. (2021).

A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

We herein employ in situ Hi-C with an auxin-inducible degron (AID) system to examine the effect of chromatin remodeling on 3D genome organization in yeast. Eight selected ATP-dependent chromatin remodelers representing various subfamilies contribute to 3D genome organization differently. Among the studied remodelers, the temporary depletions of Chd1p, Swr1p, and Sth1p (a catalytic subunit of the Remodeling the Structure of Chromatin [RSC] complex) cause the most significant defects in intra-chromosomal contacts, and the regulatory roles of these three remodelers in 3D genome organization differ depending on the chromosomal context and cell cycle stage. Furthermore, even though Chd1p and Isw1p are known to share functional similarities/redundancies, their depletions lead to distinct effects on 3D structures. The RSC and cohesin complexes also differentially modulate 3D genome organization within chromosome arm regions, whereas RSC appears to support the function of cohesin in centromeric clustering at G2 phase. Our work suggests that the ATP-dependent chromatin remodelers control the 3D genome organization of yeast through their chromatin-remodeling activities.

Application of Rhizomucor miehei lipase-displaying Pichia pastoris whole cell for biodiesel production using agro-industrial residuals as substrate

This work aimed the application of a new biocatalyst for biodiesel production from residual agro-industrial fatty acids. A recombinant Pichia pastoris displaying lipase from Rhizomucor miehei (RML) on the cell surface, using the PIR-1 anchor system, were prepared using glycerol as the carbon source. The biocatalyst, named RML-PIR1 showed optimum temperature of 45 °C (74.0 U/L). The stability tests resulted in t_1/2 of 3.49 and 2.15 h at 40 and 45 °C, respectively. RML-PIR1 was applied in esterification reactions using industrial co-products as substrates, palm fatty acid distillate (PFAD) and soybean fatty acid distillate (SFAD). The highest productivity was observed for SFAD after 48 h presenting 79.1% of conversion using only 10% of biocatalyst and free-solvent system. This is about ca. eight times higher than commercial free RML in the same conditions. The stabilizing agents study revealed that the treatment using glutaraldehyde (GA) and poly(ethylene glycol) (PEG) enabled increased stability and reuse of biocatalyst. It was observed by SEM analysis that the treatment modified the cell morphology. RML-PIR1-GA presented 87.9% of the initial activity after 6 reuses, whilst the activity of unmodified RML-PIR decreased by 40% after the first use. These results were superior to those obtained in the literature, making this new biocatalyst promising for biotechnological applications, such as the production of biofuels on a large scale.

The Genome of the CTG(Ser1) Yeast Scheffersomyces stipitis Is Plastic

Microorganisms need to adapt to environmental changes, and genome plasticity can lead to rapid adaptation to hostile environments by increasing genetic diversity. Here, we investigate genome plasticity in the CTG(Ser1) yeast Scheffersomyces stipitis, an organism with an enormous potential for second-generation biofuel production. We demonstrate that S. stipitis has an intrinsically plastic genome and that different S. stipitis isolates have genomes with distinct chromosome organizations. Real-time evolution experiments show that S. stipitis genome plasticity is common and rapid since extensive genomic changes with fitness benefits are detected following in vitro evolution experiments. Hybrid MinION Nanopore and Illumina genome sequencing identify retrotransposons as major drivers of genome diversity. Indeed, the number and position of retrotransposons are different in different S. stipitis isolates, and retrotransposon-rich regions of the genome are sites of chromosome rearrangements. Our findings provide important insights into the adaptation strategies of the CTG(Ser1) yeast clade and have critical implications in the development of second-generation biofuels. These data highlight that genome plasticity is an essential factor for developing sustainable S. stipitis platforms for second-generation biofuels production. IMPORTANCE Genomes contain genes encoding the information needed to build the organism and allow it to grow and develop. Genomes are described as stable structures where genes have specific positions within a chromosome. Changes in gene dosage and position are viewed as harmful. However, it is becoming increasingly clear that genome plasticity can benefit microbial organisms that need to adapt rapidly to environmental changes. Mechanisms of genome plasticity are still poorly understood. This study focuses on Scheffersomyces stipitis, a yeast that holds great potential for second-generation biofuel production generated from forestry and agriculture waste. We demonstrate that S. stipitis chromosomes are easily reshuffled and that chromosome reshuffling is linked to adaptation to hostile environments. Genome sequencing demonstrates that mobile genetic elements, called transposons, mediate S. stipitis genome reshuffling. These data highlight that understanding genome plasticity is important for developing sustainable S. stipitis platforms for second-generation biofuels production.

ASP-Enzymosomes with Saccharomyces cerevisiae Asparaginase II Expressed in Pichia pastoris: Formulation Design and In Vitro Studies of a Potential Antileukemic Drug

The bacterial enzyme asparaginase is the main treatment option for acute lymphoblastic leukemia. However, it causes side effects, such as immunological reactions, and presents undesirable glutaminase activity. As an alternative, we have been studying asparaginase II from Saccharomyces cerevisiae, coded by ASP3 gene, which was cloned and expressed in Pichia pastoris. The recombinant asparaginase (ASP) presented antileukemic activity and a glutaminase activity 100 times lower in comparison to its asparaginase activity. In this work, we describe the development of a delivery system for ASP via its covalent attachment to functionalized polyethylene glycol (PEG) polymer chains in the outer surface of liposomes (ASP-enzymosomes). This new delivery system demonstrated antiproliferative activity against K562 (chronic myeloid leukemia) and Jurkat (acute lymphocytic leukemia) cell lines similar to that of ASP. The antiproliferative response of the ASP-enzymosomes against the Jurkat cells suggests equivalence to that of the free Escherichia coli commercial asparaginase (Aginasa^®). Moreover, the ASP-enzymosomes were stable at 4 °C with no significant loss of activity within 4 days and retained 82% activity up to 37 days. Therefore, ASP-enzymosomes are a promising antileukemic drug.

High value-added products derived from crude glycerol via microbial fermentation using Yarrowia clade yeast

BACKGROUND

Contemporary biotechnology focuses on many problems related to the functioning of developed societies. Many of these problems are related to health, especially with the rapidly rising numbers of people suffering from civilization diseases, such as obesity or diabetes. One factor contributing to the development of these diseases is the high consumption of sucrose. A very promising substitute for this sugar has emerged: the polyhydroxy alcohols, characterized by low caloric value and sufficient sweetness to replace table sugar in food production.

RESULTS

In the current study, yeast belonging to the Yarrowia clade were tested for erythritol, mannitol and arabitol production using crude glycerol from the biodiesel and soap industries as carbon sources. Out of the 13 tested species, Yarrowia divulgata and Candida oslonensis turned out to be particularly efficient polyol producers. Both species produced large amounts of these compounds from both soap-derived glycerol (59.8-62.7 g dm-3) and biodiesel-derived glycerol (76.8-79.5 g dm-3). However, it is equally important that the protein and lipid content of the biomass (around 30% protein and 12% lipid) obtained after the processes is high enough to use this yeast in the production of animal feed.

CONCLUSIONS

The use of waste glycerol for the production of polyols as well as utilization of the biomass obtained after the process for the production of feed are part of the development of modern waste-free technologies.

Performance of xylose-fermenting yeasts in oat and soybean hulls hydrolysate and improvement of ethanol production using immobilized cell systems

We investigated the fermentation of a mixture of oat and soybean hulls (1:1) subjected to acid (AH) or enzymatic (EH) hydrolyses, with both showing high osmotic pressures (> 1200 Osm kg-1) for the production of ethanol. Yeasts of genera Spathaspora, Scheffersomyces, Sugiymaella, and Candida, most of them biodiverse Brazilian isolates and previously untested in bioprocesses, were cultivated in these hydrolysates. Spathaspora passalidarum UFMG-CM-469 showed the best ethanol production kinetics in suspended cells cultures in acid hydrolysate, under microaerobic and anaerobic conditions. This strain was immobilized in LentiKats® (polyvinyl alcohol) and cultured in AH and EH. Supplementation of hydrolysates with crude yeast extract and peptone was also performed. The highest ethanol production was obtained using hydrolysates supplemented with crude yeast extract (AH-CYE and EH-CYE) showing yields of 0.40 and 0.44 g g-1, and productivities of 0.39 and 0.29 g (L h)-1, respectively. The reuse of the immobilized cells was tested in sequential fermentations of AH-CYE, EH-CYE, and a mixture of acid and enzymatic hydrolysates (AEH-CYE) operated under batch fluidized bed, with ethanol yields ranging from 0.31 to 0.40 g g-1 and productivities from 0.14 to 0.23 g (L h)-1. These results warrant further research using Spathaspora yeasts for second-generation ethanol production.

Ester synthesis mechanism and activity by Bacillus licheniformis, Candida etchellsii, and Zygosaccharomyces rouxii isolated from Chinese horse bean chili paste

BACKGROUND

Esters are indispensable aroma compounds and contribute significantly to the fruity aromas in fermented condiments. The ester synthesis activity and pathways of Bacillus licheniformis, Candida etchellsii, and Zygosaccharomyces rouxii, isolated from Chinese horse bean chili-paste (CHCP), were investigated. Chemical buffer models containing esterification and alcoholysis systems inoculated with extracellular extracts of these three strains were established.

RESULTS

The ester synthesis activity of C. etchellsii was stronger than that of the other two strains. Zygosaccharomyces rouxii could synthesize acetate esters via esterification, whereas the biosynthesis pathways of B. licheniformis and C. etchellsii were esterification and alcoholysis. Esterification exhibited relatively high activity at pH 4, whereas alcoholysis activity improved with an increase in the pH from 4 to 8. Candida etchellsii could synthesize C₆ -C₈ of acetate esters, and its activity improved with the number of alcohol carbon atoms. These three strains could synthesize C₁₀ -C₁₈ of ethyl esters. Their ethyl ester synthesis activity decreased with the aliphatic acid carbon number.

CONCLUSION

Candida etchellsii has the potential to be used in CHCP fermentation to accumulate esters and improve flavor compared with the other two strains. This research is helpful in explaining the mechanism of ester synthesis in fermented condiments. © 2021 Society of Chemical Industry.

Modulation of heterologous protein secretion in the thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC 656 by CRISPR-Cas9 system

The thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC 656 is a potential host strain for industrial protein production. Heterologous proteins are often retained intracellularly in yeast resulting in endoplasmic reticulum (ER) stress and poor secretion, and despite efforts to engineer protein secretory pathways, heterologous protein production is often lower than expected. We hypothesized that activation of genes involved in the secretory pathway could mitigate ER stress. In this study, we created mutants defective in protein secretory-related functions using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) tools. Secretion of the model protein xylanase was significantly decreased in loss of function mutants for oxidative stress (sod1Δ) and vacuolar and protein sorting (vps1Δ and ypt7Δ) genes. However, xylanase secretion was unaffected in an autophagy related atg12Δ mutant. Then, we developed a system for sequence-specific activation of target gene expression (CRISPRa) in O. thermomethanolica and used it to activate SOD1, VPS1 and YPT7 genes. Production of both non-glycosylated xylanase and glycosylated phytase was enhanced in the gene activated mutants, demonstrating that CRISPR-Cas9 systems can be used as tools for understanding O. thermomethanolica genes involved in protein secretion, which could be applied for increasing heterologous protein secretion in this yeast.

Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

Development of wheat bran hydrolysate as Komagataella phaffii medium for heterologous protein production

Developing a Komagataella phaffii (K. phaffii, named as Pichia pastoris formerly) medium using wheat bran hydrolysate (WBH) is a potential approach for wheat bran utilization and heterologous protein by K. phaffii because K. phaffii is used as protein producer by researchers and engineers widely. In this research, the detoxification process of WBH was optimized to obtain the final procedure as pH adjusting to 10 by calcium hydroxide addition, then, 2.0 g/L active carbon absorption followed by 1 h shaking and 3,600 × g centrifugation for 10 min, finally, 3.75 mmol/L sodium thiosulfate addition for 10 min shaking followed by 3,600 × g centrifugation for 10 min. Recombinant K. phaffii-xynB harboring xylanase B gene from Aspergillus niger ATCC 1015 under alcohol oxidase 1 promoter (P_AOX1) was cultivated in detoxified WBH expressing 1059.8 U/mL xylanase B which was 90.9% of that in complex medium from Pichia protocols. These researches built a solid base for detoxified WBH as a low-cost medium of K. phaffii to express heterologous protein, also provided a bright outlet for wheat bran utilization.

The Metabolic Flux Probe (MFP)-Secreted Protein as a Non-Disruptive Information Carrier for 13C-Based Metabolic Flux Analysis

Novel cultivation technologies demand the adaptation of existing analytical concepts. Metabolic flux analysis (MFA) requires stable-isotope labeling of biomass-bound protein as the primary information source. Obtaining the required protein in cultivation set-ups where biomass is inaccessible due to low cell densities and cell immobilization is difficult to date. We developed a non-disruptive analytical concept for ¹³C-based metabolic flux analysis based on secreted protein as an information carrier for isotope mapping in the protein-bound amino acids. This “metabolic flux probe” (MFP) concept was investigated in different cultivation set-ups with a recombinant, protein-secreting yeast strain. The obtained results grant insight into intracellular protein turnover dynamics. Experiments under metabolic but isotopically nonstationary conditions in continuous glucose-limited chemostats at high dilution rates demonstrated faster incorporation of isotope information from labeled glucose into the recombinant reporter protein than in biomass-bound protein. Our results suggest that the reporter protein was polymerized from intracellular amino acid pools with higher turnover rates than biomass-bound protein. The latter aspect might be vital for ¹³C-flux analyses under isotopically nonstationary conditions for analyzing fast metabolic dynamics.

Cloning, expression in Komagataella phaffii, and biochemical characterization of recombinant sequence variants of Pseudomonas sp. S9 GDSL-esterase

Two recombinant Komagataella phaffii (formerly Pichia pastoris) yeast strains for production of two sequential variants of EstS9 esterase from psychrotolerant bacterium Pseudomonas sp. S9, i.e. αEstS9N (a two-domain enzyme consisting of a catalytic domain and an autotransporter domain) and αEstS9Δ (a single-domain esterase) were constructed. However, only one of recombinant K. phaffii strains, namely Komagataella phaffii X-33/pPICZαestS9Δ, allowed to successfully produce and secrete recombinant αEstS9Δ enzyme outside of the host cell. The purified αEstS9Δ esterase was active towards short-chain p-nitrophenyl esters (C2-C8), with optimal activity for the acetate (C2) ester. The single-domain αEstS9Δ esterase exhibits the highest activity at 60oC and pH 9.5. In addition, the enzyme retains 90% of its activity after 3 hour incubation at 70-90oC. What should be also noted is that αEstS9Δ esterase produced in the K. phaffii expression system has a much higher specific activity (0.069 U/mg of protein) than the recombinant EstS9Δ esterase produced in an E. coli expression system (0.0025 U/mg of protein) (Wicka et al., 2016, Acta Biochim Pol 63: 117-125. https://doi.org/10.18388/abp.2015_1074).

Combination of mutagenesis and adaptive evolution to engineer salt-tolerant and aroma-producing yeast for soy sauce fermentation

BACKGROUND

The moromi fermentation of high-salt liquid-state fermentation (HLF) soy sauce is usually performed in high-brine solution (17-20%, w/w), which decreases the metabolic activity of aroma-producing yeast. To enhance the soy sauce flavors, increasing the salt tolerance of aroma-producing yeasts is very important for HLF soy sauce fermentation.

RESULTS

In the present study, atmospheric and room-temperature plasma (ARTP) was first used to mutate the aroma-producing yeast Wickerhamomyces anomalus, and the salt tolerant strains were obtained by selection of synthetic medium with a sodium chloride concentration of 18% (w/w). Furthermore, adaptive laboratory evolution (ALE) was used to improve the salt tolerance of the mutant strains. The results obtained indicated that the combination use of ARTP and ALE markedly increased the NaCl tolerance of the yeast by increasing the cellular accumulation of K+ and removal of cytosolic Na+ , in addition to promoting the production of glycerin and strengthening the integrity of the cell membrane and cell wall. In soy sauce fermentation, the engineered strains improved the physicochemical parameters of HLF soy sauce compared to those produced by the wild-type strain, and the engineered strains also increased the alcohol, acid and aldehyde production, and enriched the types of esters in the soy sauce.

CONCLUSION

The results of the present study indicated that the combination of ARTP mutagenesis and ALE significantly improved the salt tolerance of the aroma-producing yeast, and also enhanced the production of volatiles of HLF soy sauce. © 2021 Society of Chemical Industry.

Analysis of N-glycosylation in fungal l-amino acid oxidases expressed in the methylotrophic yeast Pichia pastoris

l-amino acid oxidases (LAAOs) catalyze the oxidative deamination of l-amino acids to corresponding α-keto acids. Here, we describe the heterologous expression of four fungal LAAOs in Pichia pastoris. cgLAAO1 from Colletotrichum gloeosporioides and ncLAAO1 from Neurospora crassa were able to convert substrates not recognized by recombinant 9His-hcLAAO4 from the fungus Hebeloma cylindrosporum described earlier thereby broadening the substrate spectrum for potential applications. 9His-frLAAO1 from Fibroporia radiculosa and 9His-laLAAO2 from Laccaria amethystine were obtained only in low amounts. All four enzymes were N-glycosylated. We generated mutants of 9His-hcLAAO4 lacking N-glycosylation sites to further understand the effects of N-glycosylation. All four predicted N-glycosylation sites were glycosylated in 9His-hcLAAO4 expressed in P. pastoris. Enzymatic activity was similar for fully glycosylated 9His-hcLAAO4 and variants without one or all N-glycosylation sites after acid activation of all samples. However, activity without acid treatment was low in a variant without N-glycans. This was caused by the absence of a hypermannosylated N-glycan on asparagine residue N54. The lack of one or all of the other N-glycans was without effect. Our results demonstrate that adoption of a more active conformation requires a specific N-glycosylation during biosynthesis.

Production of Recombinant Human Ceruloplasmin: Improvements and Perspectives

The ferroxidase ceruloplasmin (CP) plays a crucial role in iron homeostasis in vertebrates together with the iron exporter ferroportin. Mutations in the CP gene give rise to aceruloplasminemia, a rare neurodegenerative disease for which no cure is available. Many aspects of the (patho)physiology of CP are still unclear and would benefit from the availability of recombinant protein for structural and functional studies. Furthermore, recombinant CP could be evaluated for enzyme replacement therapy for the treatment of aceruloplasminemia. We report the production and preliminary characterization of high-quality recombinant human CP in glycoengineered Pichia pastoris SuperMan5. A modified yeast strain lacking the endogenous ferroxidase has been generated and employed as host for heterologous expression of the secreted isoform of human CP. Highly pure biologically active protein has been obtained by an improved two-step purification procedure. Glycan analysis indicates that predominant glycoforms HexNAc2Hex8 and HexNAc2Hex11 are found at Asn119, Asn378, and Asn743, three of the canonical four N-glycosylation sites of human CP. The availability of high-quality recombinant human CP represents a significant advancement in the field of CP biology. However, productivity needs to be increased and further careful glycoengineering of the SM5 strain is mandatory in order to evaluate the possible therapeutic use of the recombinant protein for enzyme replacement therapy of aceruloplasminemia patients.