A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii

Allosteric Effectors Outcompete Transcript Levels and Substrate Concentration in Regulating Central Carbon Flux During the Crabtree Effect Transition

While the metabolic shift in Saccharomyces cerevisiae across the Crabtree effect is well-documented, the role of allosteric regulation in this transition remains unclear. Here, we investigated allosteric regulation by inducing a growth rate shift from 0.2 to 0.35 h. Our results revealed 35 regulatory interactions across 23 central carbon metabolism reactions, with allosteric effectors explaining 29% of flux changes-surpassing the contributions of transcript abundance and substrate concentration. Additionally, key Crabtree-responsive reactions' flux changes were co-regulated by allosteric effectors, transcript abundance, and enzyme turnover numbers. These underscore the significance of allosteric regulation in metabolic adaptation during growth rate transitions in Saccharomyces cerevisiae.

Nucleotide distribution analysis of 5'UTRs in genome-scale directs their redesign and expression regulation in yeast

Non-conventional yeasts have emerged as important sources of valuable products in bioindustries. However, tools for the control of expression are limited in these hosts. In this study, we aimed to excavate the tools for the regulation of translation that are often overlooked. 5'UTR analysis of genome-scale annotated genes of four yeast species revealed a distinct decreasing 'G' frequency in -100 ∼ -1 region from 5040 5'UTRs in Komagataella phaffii. New 5'UTRs were regenerated by base substitutions in defined regions, and replacement of 'G' by 'A' or 'T' in the -50 ∼ -1 region highly facilitated gene expression. Preference analysis of all nucleotide triplets in 5'UTRs revealed a KZ3 (-3 ∼ -1) that dominantly affected gene expression. A total of 128 KZ3 variants were constructed to work with promoters of methanol-inducible PAOX1 and constitutive PGAP, of which 58 KZ3 variants increased gene expression and maximum difference in strength was 15-fold among all variants. Polysome profiling analysis clarified that 5'UTR-KZ3 enhanced gene expression at translational but not transcriptional levels. Finally, improved production of three industrial proteins and one platform compound were achieved by ready-made 5'UTR-KZ3 or in situ modification of the 5'UTR. This study provides new references and tools for the fine-tuning of translational regulation in yeast and other fungi.

The rate of glucose metabolism sets the cell morphology across yeast strains and species

Yeasts are a diverse group of unicellular fungi that have developed a wide array of phenotypes and traits over 400 million years of evolution. However, we still lack an understanding of the biological principles governing the range of cell morphologies, metabolic modes, and reproductive strategies yeasts display. In this study, we explored the relationship between cell morphology and metabolism in sixteen yeast strains across eleven species. We performed a quantitative analysis of the physiology and morphology of these strains and discovered a strong correlation between the glucose uptake rate (GUR) and the surface-area-to-volume ratio. 14C-glucose uptake experiments demonstrated that the GUR for a given strain is governed either by glucose transport capacity or glycolytic rate, indicating that it is rather the rate of glucose metabolism in general that correlates with cell morphology. Furthermore, perturbations in glucose metabolism influenced cell sizes, whereas manipulating cell size did not affect GUR, suggesting that glucose metabolism determines cell size rather than the reverse. Across the strains tested, we also found that the rate of glucose metabolism influenced ethanol production rate, biomass yield, and carbon dioxide transfer rate. Overall, our findings demonstrate that the rate of glucose metabolism is a key factor shaping yeast cell morphology and physiology, offering new insights into the fundamental principles of yeast biology.

Impact of Oxygen Availability on the Organelle-Specific Redox Potentials and Stress in Recombinant Protein Producing Komagataella phaffii

The yeast Komagataella phaffii (syn. Pichia pastoris) is a highly effective and well-established host for the production of recombinant proteins. The redox balance of its secretory pathway, which is multi-organelle dependent, is of high importance for producing secretory proteins. Redox imbalance and oxidative stress can significantly influence protein folding and secretion. Glutathione serves as the main redox buffer of the cell and cellular redox conditions can be assessed through the status of the glutathione redox couple (GSH-GSSG). Previous research often focused on the redox potential of the endoplasmic reticulum (ER), where oxidative protein folding and disulphide bond formation occur. In this study, in vivo measurements of the glutathione redox potential were extended to different subcellular compartments by targeting genetically encoded redox sensitive fluorescent proteins (roGFPs) to the cytosol, ER, mitochondria and peroxisomes. Using these biosensors, the impact of oxygen availability on the redox potentials of the different organelles was investigated in non-producing and producing K. phaffii strains in glucose-limited chemostat cultures. It was found that the transition from normoxic to hypoxic conditions affected the redox potential of all investigated organelles, while the exposure to hyperoxic conditions did not impact them. Also, as reported previously, hypoxic conditions led to increased recombinant protein secretion. Finally, transcriptome and proteome analyses provided novel insights into the short-term response of the cells from normoxic to hypoxic conditions.

Physiological relevance, localization and substrate specificity of the alternative (type II) mitochondrial NADH dehydrogenases of Ogataea parapolymorpha

Mitochondria from Ogataea parapolymorpha harbor a branched electron-transport chain containing a proton-pumping Complex I NADH dehydrogenase and three Type II NADH dehydrogenases (NDH-2). To investigate the physiological role, localization and substrate specificity of these enzymes, the growth of various NADH dehydrogenase knockout mutants was quantitatively characterized in shake-flask and chemostat cultures, followed by oxygen-uptake experiments with isolated mitochondria. NAD(P)H:quinone oxidoreduction of the three NDH-2 were individually assessed. Our findings reveal that the O. parapolymorpha respiratory chain contains an internal NADH-accepting NDH-2 (Ndh2-1/OpNdi1), at least one external NAD(P)H-accepting enzyme, and likely additional mechanisms for respiration-linked oxidation of cytosolic NADH. Metabolic regulation appears to prevent competition between OpNdi1 and Complex I for mitochondrial NADH. With the exception of OpNdi1, the respiratory chain of O. parapolymorpha exhibits metabolic redundancy and tolerates deletion of multiple NADH-dehydrogenase genes without compromising fully respiratory metabolism.

Metabolic Engineering of Komagataella phaffii for Xylose Utilization from Cellulosic Biomass

Cellulosic biomass hydrolysates are rich in glucose and xylose, but most microorganisms, including Komagataella phaffii, are unable to utilize xylose effectively. To address this limitation, we engineered a K. phaffii strain optimized for xylose metabolism through the xylose oxidoreductase pathway and promoter optimization. A promoter library with varying strengths was used to fine-tune the expression levels of the XYL1, XYL2, and XYL3 genes, resulting in a strain with a strong promoter for XYL2 and weaker promoters for XYL1 and XYL3. This engineered strain exhibited superior growth, achieving 14 g cells/L and a maximal growth rate of 0.4 g cells/L-h in kenaf hydrolysate, outperforming a native strain by 17%. This study is the first to report the introduction of the xylose oxidoreductase pathway into K. phaffii, demonstrating its potential as an industrial platform for producing yeast protein and other products from cellulosic biomass.

From natural to synthetic: Promoter engineering in yeast expression systems

Synthetic promoters are particularly relevant for application not only in yeast expression systems designed for high-level heterologous protein production but also in other applications such as metabolic engineering, cell biological research, and stage-specific gene expression control. By designing synthetic promoters, researcher can create customized expression systems tailored to specific needs, whether it is maximizing protein production or precisely controlling gene expression at different stages of a process. While recognizing the limitations of endogenous promoters, they also provide important information needed to design synthetic promoters. In this review, emphasis will be placed on some key approaches to identify endogenous, and to generate synthetic promoters in yeast expression systems. It shows the connection between endogenous and synthetic promoters, highlighting how their interplay contributes to promoter development. Furthermore, this review illustrates recent developments in biotechnological advancements and discusses how this field will evolve in order to develop custom-made promoters for diverse applications. This review offers detailed information, explores the transition from endogenous to synthetic promoters, and presents valuable perspectives on the next generation of promoter design strategies.

Fermenting the future - on the benefits of a bioart collaboration

In this article we explore the intersection of science and art through a collaboration between us scientists and the bioartists Anna Dimitriu and Alex May, focusing on the interface of yeast biotechnology and art. The collaboration, originally initiated in 2018, resulted in three major artworks: CULTURE, depicting the evolution of yeast and human societies; FERMENTING FUTURES, illustrating a synthetic autotrophic yeast and its link to lactic acid production; and WOOD SPIRIT-AMBER ACID, inspired by the VIVALDI project targeting CO2 reduction to methanol. We emphasize the reciprocal nature of the collaboration, detailing the scientific insights gained and the impact of artistic perspectives on us as researchers. We also highlight the historical connection between art and science, particularly in the Renaissance periods, and underscore the educational value of integrating art into science not only to support public engagement and science dissemination, but also to widen our own perceptions in our research.

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.

High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux

BACKGROUND

Production of 3-hydroxypropionic acid (3-HP) through the malonyl-CoA pathway has yielded promising results in Pichia pastoris (Komagataella phaffii), demonstrating the potential of this cell factory to produce this platform chemical and other acetyl-CoA-derived products using glycerol as a carbon source. However, further metabolic engineering of the original P. pastoris 3-HP-producing strains resulted in unexpected outcomes, e.g., significantly lower product yield and/or growth rate. To gain an understanding on the metabolic constraints underlying these observations, the fluxome (metabolic flux phenotype) of ten 3-HP-producing P. pastoris strains has been characterized using a high throughput ¹³C-metabolic flux analysis platform. Such platform enabled the operation of an optimised workflow to obtain comprehensive maps of the carbon flux distribution in the central carbon metabolism in a parallel-automated manner, thereby accelerating the time-consuming strain characterization step in the design-build-test-learn cycle for metabolic engineering of P. pastoris.

RESULTS

We generated detailed maps of the carbon fluxes in the central carbon metabolism of the 3-HP producing strain series, revealing the metabolic consequences of different metabolic engineering strategies aimed at improving NADPH regeneration, enhancing conversion of pyruvate into cytosolic acetyl-CoA, or eliminating by-product (arabitol) formation. Results indicate that the expression of the POS5 NADH kinase leads to a reduction in the fluxes of the pentose phosphate pathway reactions, whereas an increase in the pentose phosphate pathway fluxes was observed when the cytosolic acetyl-CoA synthesis pathway was overexpressed. Results also show that the tight control of the glycolytic flux hampers cell growth due to limited acetyl-CoA biosynthesis. When the cytosolic acetyl-CoA synthesis pathway was overexpressed, the cell growth increased, but the product yield decreased due to higher growth-associated ATP costs. Finally, the six most relevant strains were also cultured at pH 3.5 to assess the effect of a lower pH on their fluxome. Notably, similar metabolic fluxes were observed at pH 3.5 compared to the reference condition at pH 5.

CONCLUSIONS

This study shows that existing fluoxomics workflows for high-throughput analyses of metabolic phenotypes can be adapted to investigate P. pastoris, providing valuable information on the impact of genetic manipulations on the metabolic phenotype of this yeast. Specifically, our results highlight the metabolic robustness of P. pastoris's central carbon metabolism when genetic modifications are made to increase the availability of NADPH and cytosolic acetyl-CoA. Such knowledge can guide further metabolic engineering of these strains. Moreover, insights into the metabolic adaptation of P. pastoris to an acidic pH have also been obtained, showing the capability of the fluoxomics workflow to assess the metabolic impact of environmental changes.

Metabolic engineering of the acid-tolerant yeast Pichia kudriavzevii for efficient L-malic acid production at low pH

Currently, the biological production of L-malic acid (L-MA) is mainly based on the fermentation of filamentous fungi at near-neutral pH, but this process requires large amounts of neutralizing agents, resulting in the generation of waste salts when free acid is obtained in the downstream process, and the environmental hazards associated with the waste salts limit the practical application of this process. To produce L-MA in a more environmentally friendly way, we metabolically engineered the acid-tolerant yeast Pichia kudriavzevii and achieved efficient production of L-MA through low pH fermentation. First, an initial L-MA-producing strain that relies on the reductive tricarboxylic acid (rTCA) pathway was constructed. Subsequently, the L-MA titer and yield were further increased by fine-tuning the flux between the pyruvate and oxaloacetate nodes. In addition, we found that the insufficient supply of NADH for cytoplasmic malate dehydrogenase (MDH) hindered the L-MA production at low pH, which was resolved by overexpressing the soluble pyridine nucleotide transhydrogenase SthA from E. coli. Transcriptomic and metabolomic data showed that overexpression of EcSthA contributed to the activation of the pentose phosphate pathway and provided additional reducing power for MDH by converting NADPH to NADH. Furthermore, overexpression of EcSthA was found to help reduce the accumulation of the by-product pyruvate but had no effect on the accumulation of succinate. In microaerobic batch fermentation in a 5-L fermenter, the best strain, MA009-10-URA3 produced 199.4 g/L L-MA with a yield of 0.94 g/g glucose (1.27 mol/mol), with a productivity of 1.86 g/L/h. The final pH of the fermentation broth was approximately 3.10, meaning that the amount of neutralizer used was reduced by more than 50% compared to the common fermentation processes using filamentous fungi. To our knowledge, this is the first report of the efficient bioproduction of L-MA at low pH and represents the highest yield of L-MA in yeasts reported to date.

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Enzyme turnover numbers (kcat) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally measured kcat data are sparse and noisy. Here we provide a deep learning approach (DLKcat) for high-throughput kcat prediction for metabolic enzymes from any organism merely from substrate structures and protein sequences. DLKcat can capture kcat changes for mutated enzymes and identify amino acid residues with a strong impact on kcat values. We applied this approach to predict genome-scale kcat values for more than 300 yeast species. Additionally, we designed a Bayesian pipeline to parameterize enzyme-constrained genome-scale metabolic models from predicted kcat values. The resulting models outperformed the corresponding original enzyme-constrained genome-scale metabolic models from previous pipelines in predicting phenotypes and proteomes, and enabled us to explain phenotypic differences. DLKcat and the enzyme-constrained genome-scale metabolic model construction pipeline are valuable tools to uncover global trends of enzyme kinetics and physiological diversity, and to further elucidate cellular metabolism on a large scale.

Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production

Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.

Innovative Bioprocess Strategies Combining Physiological Control and Strain Engineering of Pichia pastoris to Improve Recombinant Protein Production

The combination of strain and bioprocess engineering strategies should be considered to obtain the highest levels of recombinant protein production (RPP) while assuring product quality and process reproducibility of heterologous products. In this work, two complementary approaches were investigated to improve bioprocess efficiency based on the yeast P. pastoris. Firstly, the performance of two Candida rugosa lipase 1 producer clones with different gene dosage under the regulation of the constitutive P_GAP were compared in chemostat cultures with different oxygen-limiting conditions. Secondly, hypoxic conditions in carbon-limited fed-batch cultures were applied by means of a physiological control based on the respiratory quotient (RQ). Stirring rate was selected to maintain RQ between 1.4 and 1.6, since it was found to be the most favorable in chemostat. As the major outcome, between 2-fold and 4-fold higher specific production rate (q_P) values were observed when comparing multicopy clone (MCC) and single-copy clone (SCC), both in chemostat and fed-batch. Additionally, when applying oxygen limitation, between 1.5-fold and 3-fold higher q_P values were obtained compared with normoxic conditions. Thus, notable increases of up to 9-fold in the production rates were reached. Furthermore, transcriptional analysis of certain key genes related to RPP and central carbon metabolism were performed. Results seem to indicate the presence of a limitation in post-transcriptional protein processing steps and a possible transcription attenuation of the target gene in the strains with high gene dosage. The entire approach, including both strain and bioprocess engineering, represents a relevant novelty involving physiological control in Pichia cell factory and is of crucial interest in bioprocess optimization, boosting RPP, allowing bioproducts to be economically competitive in the market, and helping develop the bioeconomy.

Strains and Molecular Tools for Recombinant Protein Production in Pichia pastoris

Within the last two decades, the methylotrophic yeast Pichia pastoris (Komagataella phaffii) has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.

The evolution of the GALactose utilization pathway in budding yeasts

The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker's yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the sugar galactose for energy and biomass production. The GAL pathway has long served as a model system for understanding how eukaryotic metabolic pathways, including their modes of regulation, evolve. More recently, the physical linkage of the structural genes GAL1, GAL7, and GAL10 in diverse budding yeast genomes has been used as a model for understanding the evolution of gene clustering. In this review, we summarize exciting recent work on three different aspects of this iconic pathway's evolution: gene cluster organization, GAL gene regulation, and the population genetics of the GAL pathway.

What makes Komagataella phaffii non-conventional?

The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.

Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.

Hybrid-architectured promoter design to engineer expression in yeast

Engineered promoters are key components that allow engineered expression of genes in the cell-factory design. Promoters having exceptional strength are attractive candidates for designing metabolic engineering strategies for tailoring de novo production strategies that require directed evolution methods by engineering with de novo synthetic biology tools. Engineered promoter variants (EPVs) of naturally occurring promoters (NOPs) can be designed using metabolic engineering strategies and synthetic biology tools if the genes encoding the activating transcription factors (TFs) exist in the genome and are expressed and synthesized at non-limiting concentrations within the cell. The hybrid-architectured EPV design method targets an essential and predetermined part of the general transcription machinery. That is cis-acting DNA site(s) in coordination with the trans-acting factor(s) that must bind for the regulated transcription machinery activation. The method needs genomic and functional information that can lead to the discovery of the master TF(s) and synthetic cis-acting DNA elements, enabling the engineering of binding of master regulator TF(s). The method aims to generate EPVs that combine the advantages of being an exceptional stronger EPV(s) than the NOPs and permit "green-and-clean production" on a non-toxic carbon source, such as ethanol or glucose. By introducing our recent work on the engineering of ADH2 hybrid-promoter architectures to enhance recombinant protein expression on ethanol, we provide the method and protocol for the design of ADH2 hybrid-promoter architectures that can be adapted to other promoters in different substrate utilization pathways in Pichia pastoris (syn. Komagataella phaffii), as well as in other yeasts.

Fermenting Futures: an artistic view on yeast biotechnology

BioArt is a new discipline where artists employ materials and techniques of modern life sciences and create novel meanings of biology, often involving living organisms such as tissue culture, bacteria and yeasts, which may also be genetically engineered. The authors have engaged in a collaboration to develop 'Fermenting Futures', a project designed to explore the significance of yeast for early human history by enabling baking and brewing, all the way to industrial biotechnology and synthetic biology with their potential contributions to fight the climate change. Research in two of the authors' lab provides the materials and thematic lines for the artists to develop their installations. The two main pieces reflect on fermentation as a metabolic trait of baker's yeast and its enormous transformational power for human society, and on the application of synthetic biology to enable yeast to grow and produce materials from carbon dioxide. The role of BioArt to support public engagement and science dissemination is discussed, highlighting the importance of collaborations of scientists and artists on equal terms, as showcased here.

Enhanced Recombinant Protein Production Under Special Environmental Stress

Regardless of bacteria or eukaryotic microorganism hosts, improving their ability to express heterologous proteins is always a goal worthy of elaborate study. In addition to traditional methods including intracellular synthesis process regulation and extracellular environment optimization, some special or extreme conditions can also be employed to create an enhancing effect on heterologous protein production. In this review, we summarize some extreme environmental factors used for the improvement of heterologous protein expression, including low temperature, hypoxia, microgravity and high osmolality. The applications of these strategies are elaborated with examples of well-documented studies. We also demonstrated the confirmed or hypothetical mechanisms of environment stress affecting the host behaviors. In addition, multi-omics techniques driving the stress-responsive research for construction of efficient microbial cell factories are also prospected at the end.

Beyond alcohol oxidase: the methylotrophic yeast Komagataella phaffii utilizes methanol also with its native alcohol dehydrogenase Adh2

Methylotrophic yeasts are considered to use alcohol oxidases to assimilate methanol, different to bacteria which employ alcohol dehydrogenases with better energy conservation. The yeast Komagataella phaffii carries two genes coding for alcohol oxidase, AOX1 and AOX2. The deletion of the AOX1 leads to the Mut^S phenotype and the deletion of AOX1 and AOX2 to the Mut^– phenotype. The Mut^– phenotype is commonly regarded as unable to utilize methanol. In contrast to the literature, we found that the Mut^– strain can consume methanol. This ability was based on the promiscuous activity of alcohol dehydrogenase Adh2, an enzyme ubiquitously found in yeast and normally responsible for ethanol consumption and production. Using ¹³C labeled methanol as substrate we could show that to the largest part methanol is dissimilated to CO₂ and a small part is incorporated into metabolites, the biomass, and the secreted recombinant protein. Overexpression of the ADH2 gene in K. phaffii Mut^– increased both the specific methanol uptake rate and recombinant protein production, even though the strain was still unable to grow. These findings imply that thermodynamic and kinetic constraints of the dehydrogenase reaction facilitated the evolution towards alcohol oxidase-based methanol metabolism in yeast.

Komagataella phaffii as Emerging Model Organism in Fundamental Research

Komagataella phaffii (Pichia pastoris) is one of the most extensively applied yeast species in pharmaceutical and biotechnological industries, and, therefore, also called the biotech yeast. However, thanks to more advanced strain engineering techniques, it recently started to gain attention as model organism in fundamental research. So far, the most studied model yeast is its distant cousin, Saccharomyces cerevisiae. While these data are of great importance, they limit our knowledge to one organism only. Since the divergence of the two species 250 million years ago, K. phaffii appears to have evolved less rapidly than S. cerevisiae, which is why it remains more characteristic of the common ancient yeast ancestors and shares more features with metazoan cells. This makes K. phaffii a valuable model organism for research on eukaryotic molecular cell biology, a potential we are only beginning to fully exploit. As methylotrophic yeast, K. phaffii has the intriguing property of being able to efficiently assimilate methanol as a sole source of carbon and energy. Therefore, major efforts have been made using K. phaffii as model organism to study methanol assimilation, peroxisome biogenesis and pexophagy. Other research topics covered in this review range from yeast genetics including mating and sporulation behavior to other cellular processes such as protein secretion, lipid biosynthesis and cell wall biogenesis. In this review article, we compare data obtained from K. phaffii with S. cerevisiae and other yeasts whenever relevant, elucidate major differences, and, most importantly, highlight the big potential of using K. phaffii in fundamental research.

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.

Genetic engineering of an industrial yeast Candida glycerinogenes for efficient production of 2-phenylethanol

Microbial cell factories offer an economic approach for synthesizing "natural'" aromatic flavor compounds. During their fermentation process, the inefficient synthesis pathway and product cytotoxicity are the major barriers to the high-level production. This study combined metabolic engineering and tolerance engineering strategies to maximize the valuable rose-smell 2-phenylethanol (2-PE) production in Candida glycerinogenes, a GRAS diploid industrial yeast. Firstly, 2-PE metabolic networks involved in Ehrlich pathway were stepwise rewired using metabolic engineering, including the following: (1) overexpressing L-phenylalanine permease Aap9 enhanced precursor uptake; (2) overexpressing enzymes (aminotransferase Aro9 and decarboxylase Aro10) of Ehrlich pathway increased catalytic efficiency; and (3) disrupting the formation of by-product phenylacetate catalyzed by Ald2 and Ald3 maximized the metabolic flux toward 2-PE. Then, tolerance engineering was applied by overexpression of a stress-inducible gene SLC1 in the metabolically engineered strain to further enhance 2-PE production. Combining these two approaches finally resulted in 5.0 g/L 2-PE in shake flasks, with productivity reaching 0.21 g/L/h, which were increased by 38.9% and 177% compared with those of the non-engineered strain, respectively. The 2-PE yield of this engineered strain was 0.71 g/g L-phenylalanine, corresponding to 95.9% of theoretical yield. This study provides a reference to efficiently engineering of microbial cell factories for other valuable aromatic compounds. KEY POINTS: • Metabolic engineering improved 2-PE biosynthesis. • Tolerance engineering alleviated product inhibition, contributing to 2-PE production. • The best strain produced 5.0 g/L 2-PE with 0.959 mol/mol yield and high productivity.

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family

Many yeasts differentiate into multicellular phenotypes in adverse environmental conditions. Here, we investigate pseudohyphal growth in Komagataella phaffii and the involvement of the flocculin (FLO) gene family in its regulation. The K. phaffii FLO family consists of 13 members, and the conditions inducing pseudohyphal growth are different from Saccharomyces cerevisiae. So far, this phenotype was only observed when K. phaffii was cultivated at slow growth rates in glucose-limited chemostats, but not upon nitrogen starvation or the presence of fusel alcohols. Transcriptional analysis identified that FLO11, FLO400 and FLO5-1 are involved in the phenotype, all being controlled by the transcriptional regulator Flo8. The three genes exhibit a complex mechanism of expression and repression during transition from yeast to pseudohyphal form. Unlike in S. cerevisiae, deletion of FLO11 does not completely prevent the phenotype. In contrast, deletion of FLO400 or FLO5-1 prevents pseudohyphae formation, and hampers FLO11 expression. FAIRE-Seq data shows that the expression and repression of FLO400 and FLO5-1 are correlated to open or closed chromatin regions upstream of these genes, respectively. Our findings indicate that K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 upon glucose limitation in chemostats at slow growth and chromatin modulation is involved in the regulation of their expression.

Transcriptional regulatory proteins in central carbon metabolism of Pichia pastoris and Saccharomyces cerevisiae

System-wide interactions in living cells and discovery of the diverse roles of transcriptional regulatory proteins that are mediator proteins with catalytic domains and regulatory subunits and transcription factors in the cellular pathways have become crucial for understanding the cellular response to environmental conditions. This review provides information for future metabolic engineering strategies through analyses on the highly interconnected regulatory networks in Saccharomyces cerevisiae and Pichia pastoris and identifying their components. We discuss the current knowledge on the carbon catabolite repression (CCR) mechanism, interconnecting regulatory system of the central metabolic pathways that regulate cell metabolism based on nutrient availability in the industrial yeasts. The regulatory proteins and their functions in the CCR signalling pathways in both yeasts are presented and discussed. We highlight the importance of metabolic signalling networks by signifying ways on how effective engineering strategies can be designed for generating novel regulatory circuits, furthermore to activate pathways that reconfigure the network architecture. We summarize the evidence that engineering of multilayer regulation is needed for directed evolution of the cellular network by putting the transcriptional control into a new perspective for the regulation of central carbon metabolism of the industrial yeasts; furthermore, we suggest research directions that may help to enhance production of recombinant products in the widely used, creatively engineered, but relatively less studied P. pastoris through de novo metabolic engineering strategies based on the discovery of components of signalling pathways in CCR metabolism. KEY POINTS: • Transcriptional regulation and control is the key phenomenon in the cellular processes. • Designing de novo metabolic engineering strategies depends on the discovery of signalling pathways in CCR metabolism. • Crosstalk between pathways occurs through essential parts of transcriptional machinery connected to specific catalytic domains. • In S. cerevisiae, a major part of CCR metabolism is controlled through Snf1 kinase, Glc7 phosphatase, and Srb10 kinase. • In P. pastoris, signalling pathways in CCR metabolism have not yet been clearly known yet. • Cellular regulations on the transcription of promoters are controlled with carbon sources.

Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory

The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and ¹³C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

Cells balance glycolysis with respiration to support their metabolic needs in different environmental or physiological contexts. With abundant glucose, many cells prefer to grow by aerobic glycolysis or fermentation. Using 161 natural isolates of fission yeast, we investigated the genetic basis and phenotypic effects of the fermentation-respiration balance. The laboratory and a few other strains depended more on respiration. This trait was associated with a single nucleotide polymorphism in a conserved region of Pyk1, the sole pyruvate kinase in fission yeast. This variant reduced Pyk1 activity and glycolytic flux. Replacing the "low-activity" pyk1 allele in the laboratory strain with the "high-activity" allele was sufficient to increase fermentation and decrease respiration. This metabolic rebalancing triggered systems-level adjustments in the transcriptome and proteome and in cellular traits, including increased growth and chronological lifespan but decreased resistance to oxidative stress. Thus, low Pyk1 activity does not lead to a growth advantage but to stress tolerance. The genetic tuning of glycolytic flux may reflect an adaptive trade-off in a species lacking pyruvate kinase isoforms.

Identification of major ADH genes in ethanol metabolism of Pichia pastoris

The methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii) is a successful host widely used in recombinant protein production. The widespread use of a methanol-regulated alcohol oxidase 1 (AOX1) promoter for recombinant protein production has directed studies particularly about methanol metabolism in this yeast. Although there is comprehensive knowledge about methanol metabolism, there are other mechanisms in P. pastoris that have not been investigated yet, such as ethanol metabolism. The gene responsible for the consumption of ethanol ADH2 (XM_002491337, known as ADH3) was identified and characterized in our previous study. In this study, the ADH genes (XM_002489969, XM_002491163, XM_002493969) in P. pastoris genome were investigated to determine their roles in ethanol production by gene disruption analysis. We report that the ADH900 (XM_002491163) is the main gene responsible for ethanol production in P. pastoris. The ADH2 gene, previously identified as the only gene responsible for ethanol consumption, also plays a minor role in ethanol production in the absence of the ADH900 gene. The investigation of the carbon source regulation mechanism has also revealed that the ADH2 gene exhibit similar expression behaviours with ADH900 on glucose, glycerol, and methanol, however, it is strongly induced by ethanol.

GC-QTOFMS with a low-energy electron ionization source for advancing isotopologue analysis in 13C-based metabolic flux analysis

For the study of different levels of (intra)cellular regulation and condition-dependent insight into metabolic activities, fluxomics experiments based on stable isotope tracer experiments using ¹³C have become a well-established approach. The experimentally obtained non-naturally distributed ¹³C labeling patterns of metabolite pools can be measured by mass spectrometric detection with front-end separation and can be consequently incorporated into biochemical network models. Here, despite a tedious derivatization step, gas chromatographic separation of polar metabolites is favorable because of the wide coverage range and high isomer separation efficiency. However, the typically employed electron ionization energy of 70 eV leads to significant fragmentation and consequently only low-abundant ions with an intact carbon backbone. Since these ions are considered a prerequisite for the analysis of the non-naturally distributed labeling patterns and further integration into modeling strategies, a softer ionization technique is needed. In the present work, a novel low energy electron ionization source is optimized for the analysis of primary metabolites and compared with a chemical ionization approach in terms of trueness, precision, and sensitivity.