Production of Aspergillus niger β-mannosidase in Pichia pastoris

Understanding exopolysaccharide byproduct formation in Komagataella phaffii fermentation processes for recombinant protein production

BACKGROUND

Komagataella phaffii (Pichia pastoris) has emerged as a common and robust biotechnological platform organism, to produce recombinant proteins and other bioproducts of commercial interest. Key advantage of K. phaffii is the secretion of recombinant proteins, coupled with a low host protein secretion. This facilitates downstream processing, resulting in high purity of the target protein. However, a significant but often overlooked aspect is the presence of an unknown polysaccharide impurity in the supernatant. Surprisingly, this impurity has received limited attention in the literature, and its presence and quantification are rarely addressed.

RESULTS

This study aims to quantify this exopolysaccharide in high cell density recombinant protein production processes and identify its origin. In stirred tank fed-batch fermentations with a maximal cell dry weight of 155 g/L, the polysaccharide concentration in the supernatant can reach up to 8.7 g/L. This level is similar to the achievable target protein concentration. Importantly, the results demonstrate that exopolysaccharide production is independent of the substrate and the protein production process itself. Instead, it is directly correlated with biomass formation and proportional to cell dry weight. Cell lysis can confidently be ruled out as the source of this exopolysaccharide in the culture medium. Furthermore, the polysaccharide secretion can be linked to a mutation in the HOC1 gene, featured by all derivatives of strain NRRL Y-11430, leading to a characteristic thinner cell wall.

CONCLUSIONS

This research sheds light on a previously disregarded aspect of K. phaffii fermentations, emphasizing the importance of monitoring and addressing the exopolysaccharide impurity in biotechnological applications, independent of the recombinant protein produced.

Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry

In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.

Efficient expression of a novel thermophilic fungal β-mannosidase from Lichtheimia ramosa with broad-range pH stability and its synergistic hydrolysis of locust bean gum

β-Mannosidase (EC 3.2.1.25) is an exoglycosidase specific for the hydrolysis of terminal β-1,4-glycosidic linkage in mannan which can be applied in the food manufacture, animal feed, bioethanol making and coffee extraction industries. A novel β-mannosidase gene (Lrman5A) from Lichtheimia ramosa was synthesized and recombinantly expressed in Pichia pastoris X33. Lrman5A encodes 444 amino acids with a calculated molecular mass of 51.0 kDa which shares the highest identity (73%) with the β-mannosidase from Rhizomucor miehei. Purified recombinant Lrman5A showed the maximal activity at pH 6.0 and 65°C, had broad-range pH stability (retaining >65% activity after incubation at pH 3.0-8.5 at 37°C for 24 h), and was highly thermostable (retaining >80% activity after incubation at 65°C for 10 min). The specific activity, and K_m of Lrman5A was 17.5 U/mg and 1.377 mM, respectively. Lrman5A and GH5 β-mannanase displayed significant synergistic effects on the degradation of locust bean gum (LBG) and released more mannose (up to 2.89 folds) by simultaneous or sequential addition. Due to its hydrolytic properties, Lrman5A may have potential applications in the area of bioenergy, feed and food processing.

Microbial β-mannosidases and their industrial applications

Heteropolymers of mannan are polysaccharide components of the plant cell wall of gymnosperms and some angiosperms, including palm trees (Arecales and Monocot). Degradation of the complex structure of these polysaccharides requires the synergistic action of enzymes that disrupt the internal carbon skeleton of mannan and accessory enzymes that remove side chain substituents. However, complete degradation of these polysaccharides is carried out by an exo-hydrolase termed β-mannosidase. Microbial β-mannosidases belong to families 1, 2, and 5 of glycosyl hydrolases, and catalyze the hydrolysis of non-reducing ends of mannose oligomers. Besides, these enzymes are also involved in transglycosylation reactions. Because of their activity at different temperatures and pH values, these enzymes are used in a variety of industrial applications and the pharmaceutical, food, and biofuel industries.

A Recombinant Highly Thermostable β-Mannanase (ReTMan26) from Thermophilic Bacillus subtilis (TBS2) Expressed in Pichia pastoris and Its pH and Temperature Stability

A gene encoding a highly thermostable β-mannanase from a thermophilic Bacillus subtilis (TBS2) was successfully expressed in Pichia pastoris. The maximum activity of the recombinant thermostable β-mannanase (ReTMan26) was 5435 U/mL, which was obtained by high-density, fed-batch cultivation after 168-h induction with methanol in a 50-L bioreactor. The protein yield reached 3.29 mg/mL, and the protein had a molecular weight of ~42 kDa. After fermentation, ReTMan26 was purified using a 10-kDa cut-off membrane and Sephadex G-75 column. The pH and temperature optima of purified ReTMan26 were pH 6.0 and 60 °C, respectively, and the enzyme was stable at pH 2.0-8.0 and was active at 20-100 °C. HPLC analysis of the products of locust bean gum hydrolysis showed that the mannan-oligosaccharide content was 62.5%. ReTMan26 retained 58.6% of its maximum activity after treatment at 100 °C for 10 min, which was higher than any other β-mannanase reported up to now, suggesting its potential for industrial applications.

Expression of a β-mannosidase from Paenibacillus polymyxa A-8 in Escherichia coli and characterization of the recombinant enzyme

Paenibacillus polymyxa A-8, which secretes β-mannosidase, was isolated from the soil sample under a pine tree located in the "Laoban" mountain region of Sichuan, China. The β-mannosidase gene (MANB) was isolated from P. polymyxa A-8, using primers according to the complete genome. The MANB (2,550 bp) encoding 849 amino acid residues was expressed in Escherichia coli. The specific activities of β-mannosidase produced by P. polymyxa A-8 and E. coli pET30a-MANB were 12 nkat/mg and 635 nkat/mg respectively. SDS-PAGE analysis indicated that the molecular mass of the recombinant MANB was approximately 96 kDa. The recombinant MANB was active between pH 7.0-8.5 with the maximum activity at pH 7.0. It had good pH stability and adaptability. The MANB had the optimal temperature of 35°C and was relatively stable at 35-40°C. In addition, the MANB activity was enhanced by K+, Ca2+, Mn2+, and Mg2+ and inhibited by Zn2+, Cu2+, and Hg2+.

Crystallization and preliminary X-ray crystallographic analysis of recombinant β-mannosidase from Aspergillus niger

β-Mannosidase (EC 3.2.1.25) is an important exoglycosidase specific for the hydrolysis of terminal β-linked mannoside in various oligomeric saccharide structures. β-Mannosidase from Aspergillus niger was expressed in Pichia pastoris and purified to clear homogeneity. β-Mannosidase was crystallized in the presence of D-mannose and the crystal diffracted to 2.41 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a=62.37, b=69.73, c=69.90 Å, α=108.20, β=101.51, γ=103.20°. The parameters derived from the data collection indicate the presence of one molecule in the asymmetric unit.