Engineering the regulatory site of the catalase promoter for improved heterologous protein production in Pichia pastoris

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.

Enhanced Expression of Alcohol Dehydrogenase I in Pichia pastoris Reduces the Content of Acetaldehyde in Wines

Acetaldehyde is an important carbonyl compound commonly detected in wines. A high concentration of acetaldehyde can affect the flavor of wines and result in adverse effects on human health. Alcohol dehydrogenase I (ADH1) in Saccharomyces cerevisiae catalyzes the reduction reaction of acetaldehyde into ethanol in the presence of cofactors, showing the potential to reduce the content of acetaldehyde in wines. In this study, ADH1 was successfully expressed in Pichia pastoris GS115 based on codon optimization. Then, the expression level of ADH1 was enhanced by replacing its promoter with optimized promoters and increasing the copy number of the expression cassette, with ADH1 being purified using nickel column affinity chromatography. The enzymatic activity of purified ADH1 reached 605.44 ± 44.30 U/mg. The results of the effect of ADH1 on the content of acetaldehyde in wine revealed that the acetaldehyde content of wine samples was reduced from 168.05 ± 0.55 to 113.17 ± 6.08 mg/L with the addition of 5 mM NADH and the catalysis of ADH1, and from 135.53 ± 4.08 to 52.89 ± 2.20 mg/L through cofactor regeneration. Our study provides a novel approach to reducing the content of acetaldehyde in wines through enzymatic catalysis.

Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories

Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.

Expanding the promoter toolbox for metabolic engineering of methylotrophic yeasts

Methylotrophic yeasts have been widely recognized as a promising host for production of recombinant proteins and value-added chemicals. Promoters for controlled gene expression are critical for construction of efficient methylotrophic yeasts cell factories. Here, we summarized recent advances in characterizing and engineering promoters in methylotrophic yeasts, such as Komagataella phaffii and Ogataea polymorpha. Constitutive and inducible promoters controlled by methanol or other inducers/repressors were introduced to demonstrate their applications in production of proteins and chemicals. Furthermore, efforts of promoter engineering, including site-directed mutagenesis, hybrid promoter, and transcription factor regulation to expand the promoter toolbox were also summarized. This mini-review also provides useful information on promoters for the application of metabolic engineering in methylotrophic yeasts. KEY POINTS: • The characteristics of six methylotrophic yeasts and their promoters are described. • The applications of Komagataella phaffii and Ogataea polymorpha in metabolic engineeringare expounded. • Three promoter engineering strategies are introduced in order to expand the promoter toolbox.

Engineering of the CMV promoter for controlled expression of recombinant genes in HEK293 cells

Expression of recombinant genes in HEK293 cells is frequently utilized for production of recombinant proteins and viral vectors. These systems frequently employ the cytomegalovirus (CMV) promoter to drive recombinant gene transcription. However, the mechanistic basis of CMV-mediated transcriptional activation in HEK293 cells is unknown and consequently there are no strategies to engineer CMV for controlled expression of recombinant genes. Extensive bioinformatic analyses of transcription factor regulatory elements (TFREs) within the human CMV sequence and transcription factor mRNAs within the HEK293 transcriptome revealed 80 possible regulatory interactions. Through in vitro functional testing using reporter constructs harboring discrete TFREs or CMV deletion variants we identified key TFRE components and clusters of TFREs (cis-regulatory modules) within the CMV sequence. Our data reveal that CMV activity in HEK293 cells is a function of the promoters various constituent TFREs including AhR:ARNT, CREB, E4F, Sp1, ZBED1, JunB, c-Rel, and NF-κB. We also identified critical Sp1-dependent upstream activator elements near the transcriptional start site that were required for efficient transcription and YY1 and RBP-Jκ binding sites that mediate transrepression. Our study shows for the first time that novel, compact CMV-derived promoters can be engineered that exhibit up to 50% higher transcriptional efficiency (activity per unit DNA sequence) or 14% increase in total activity compared to the wild-type counterpart.

Development of synthetic biology tools to engineer Pichia pastoris as a chassis for the production of natural products

The methylotrophic yeast Pichia pastoris (a.k.a. Komagataella phaffii) is one of the most commonly used hosts for industrial production of recombinant proteins. As a non-conventional yeast, P. pastoris has unique biological characteristics and its expression system has been well developed. With the advances in synthetic biology, more efforts have been devoted to developing P. pastoris into a chassis for the production of various high-value compounds, such as natural products. This review begins with the introduction of synthetic biology tools for the engineering of P. pastoris, including vectors, promoters, and terminators for heterologous gene expression as well as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated System (CRISPR/Cas) for genome editing. This review is then followed by examples of the production of value-added natural products in metabolically engineered P. pastoris strains. Finally, challenges and outlooks in developing P. pastoris as a synthetic biology chassis are prospected.

Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts

Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using ¹³C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.

Molecular Decoration of Ceramic Supports for Highly Effective Enzyme Immobilization-Material Approach

A highly effective method was developed to functionalize ceramic supports (Al₂O₃ powders and membranes) using newly synthesized spacer molecules. The functionalized materials were subsequently utilized for Candida antarctica lipase B enzyme immobilization. The objective is to systematically evaluate the impact of various spacer molecules grafted onto the alumina materials will affect both the immobilization of the enzymes and specific material surface properties, critical to enzymatic reactors performance. The enzyme loading was significantly improved for the supports modified with shorter spacer molecules, which possessed higher grafting effectiveness on the order of 90%. The specific enzyme activity was found to be much higher for samples functionalized with longer modifiers yielding excellent enantioselectivity >97%. However, the enantiomeric ratio of the immobilized lipase was slightly lower in the case of shorter spacer molecules.