Yeast Systems Biology: Model Organism and Cell Factory

Improved biosynthesis of tyrosol by epigenetic modification-based regulation and metabolic engineering in Saccharomyces cerevisiae

Aromatic amino acids and their derivatives are high value chemicals widely used in food, pharmaceutical and feed industries. Current preparation methods for aromatic amino acid products are fraught with limitations. In this study, the efficient biosynthesis of aromatic amino acid compound tyrosol was investigated by epigenetic modification-based regulation and optimization of the biosynthetic pathway of aromatic amino acids. The production of tyrosol was significantly improved by the overexpression of m6A modification writer Ime4 and reader Pho92, and the positive regulator Gcr2. Introduction of Bbxfpk and deletion of Gpp1 further improved tyrosol production. Then the feedback inhibition of the shikimate pathway was relieved by the mutants Aro4K229L and Aro7G141S. The final tyrosol producing engineered strain was constructed by the deletion of PHA2, replacement of the native promoter of ARO10 with the strong promoter PGK1p, and introduction of tyrosine decarboxylase PcAAS. In the background of m6A modification regulation, this strain ultimately produced 954.69 ± 43.72mg/L of tyrosol, promoted by 61.7-fold in shake-flask fermentation.

Mitigating methylglyoxal-induced glycation stress: the protective role of iron, copper, and manganese coordination compounds in Saccharomyces cerevisiae

Glycation-induced stress (G-iS) is a physiological phenomenon that leads to the formation of advanced glycation end-products, triggering detrimental effects such as oxidative stress, inflammation, and damage to intracellular structures, tissues, and organs. This process is particularly relevant because it has been associated with various human pathologies, including cancer, neurodegenerative diseases, and diabetes. As therapeutic alternatives, coordination compounds with antioxidant activity show promising potential due to their versatility in attenuating oxidative stress and inflammation. Herein, we investigated the antioxidant-related protective potential of a series of complexes: [Cu(II)(BMPA)Cl2] (1), [Fe(III)(BMPA)Cl3] (2), and [Cl(BMPA)MnII-(μ-Cl)2-MnII(BMPA)-(μ-Cl)- MnII(BMPA)(Cl)2]•5H2O (3), all synthesized with the ligand bis-(2-pyridylmethyl)amine (BMPA) in Saccharomyces cerevisiae exposed to G-iS caused by methylglyoxal (MG). Pre- treatment with complexes 1-3 proved highly effective, increasing yeast tolerance to G-iS and attenuating mitochondrial dysfunction. This observed phenotype appears to result from a reduction in intracellular oxidation, lipid peroxidation levels, and glycation. Additionally, an increase in the activity of the antioxidant enzymes superoxide dismutase and catalase was observed following treatment with complexes 1-3. Notably, although complexes 1-3 provided significant protection against oxidative stress induced by H2O2 and menadione, their protective role was more effective against MG-induced glycation stress. Our results indicate that these complexes possess both antiglycation and antioxidant properties, warranting further investigation as potential interventions for mitigating glycation and oxidative stress-related pathologies.

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products

Microbial genetic circuits are vital for regulating gene expression and synthesizing bioactive compounds. However, assessing their strength and timing, especially in multicellular fungi, remains challenging. Here, an advanced microfluidic platform is combined with a mathematical model enabling precise characterization of fungal gene regulatory circuits (GRCs) at the single-cell level. Utilizing this platform, the expression intensity and timing of 30 transcription factor-promoter combinations derived from two representative fungal GRCs, using the model fungus Aspergillus nidulans are determined. As a proof of concept, the selected GRC combination is utilized to successfully refactor the biosynthetic pathways of bioactive molecules, precisely control their production, and activate the expression of the silenced biosynthetic gene clusters (BGCs). This study provides insights into microbial gene regulation and highlights the potential of platform in fungal synthetic biology applications and the discovery of novel natural products.

Critical role of model organism selection in assessing weak urban electromagnetic field effects: Implications for human health

The impact of electromagnetic fields on human health has been investigated in recent years using various model organisms, yet the findings remain unclear. In our work, we examined the effect of less-explored, weak electromagnetic fields commonly found in the urban environments we inhabit. We studied different impacts of electromagnetic fields with a frequency of 50 Hz and a combination of 50 Hz and 150 Hz, on both yeasts (Saccharomyces cerevisiae) and human macrophages. We determined growth, survival, and protein composition (SDS-PAGE) (Saccharomyces cerevisiae) and morphology of macrophages (human monocytic cell line). In yeast, the sole observed change after 24 h of exposure was the extension of the exponential growth phase by 17 h. Conversely, macrophages exhibited morphological transformations from the anti-inflammatory to the pro-inflammatory type within just 2 h of exposure to the electromagnetic field. Our results suggest that effects of electromagnetic field largely depend on the model organism. The selection of an appropriate model organism proves essential for the study of the specific impacts of electromagnetic fields. The potential risk associated with the presence of pro-inflammatory M1 macrophages in everyday urban environments primarily arises from the continual promotion of inflammatory reactions within a healthy organism and deserves further investigation.

Inorganic nitrogen inhibits symbiotic nitrogen fixation through blocking NRAMP2-mediated iron delivery in soybean nodules

Symbiotic nitrogen fixation (SNF) in legume-rhizobia serves as a sustainable source of nitrogen (N) in agriculture. However, the addition of inorganic N fertilizers significantly inhibits SNF, and the underlying mechanisms remain not-well understood. Here, we report that inorganic N disrupts iron (Fe) homeostasis in soybean nodules, leading to a decrease in SNF efficiency. This disruption is attributed to the inhibition of the Fe transporter genes Natural Resistance-Associated Macrophage Protein 2a and 2b (GmNRAMP2a&2b) by inorganic N. GmNRAMP2a&2b are predominantly localized at the tonoplast of uninfected nodule tissues, affecting Fe transfer to infected cells and consequently, modulating SNF efficiency. In addition, we identified a pair of N-signal regulators, nitrogen-regulated GARP-type transcription factors 1a and 1b (GmNIGT1a&1b), that negatively regulate the expression of GmNRAMP2a&2b, which establishes a link between N signaling and Fe homeostasis in nodules. Our findings reveal a plausible mechanism by which soybean adjusts SNF efficiency through Fe allocation in response to fluctuating inorganic N conditions, offering valuable insights for optimizing N and Fe management in legume-based agricultural systems.

Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast

Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.

Virulence and proteomic responses of Metarhizium anisopliae against Aedes albopictus larvae

The tropical climate in Malaysia provides an ideal environment for the rapid proliferation of Aedes mosquitoes, notably Aedes aegypti and Aedes albopictus, prominent vectors of dengue fever. Alarmingly, these species are increasingly developing resistance to conventional pesticides. This study aimed to evaluate the efficacy of Metarhizium anisopliae isolate HSAH5 spores, specifically on conidia (CO) and blastospores (BL), against Ae. albopictus larvae. The study centered on evaluating their pathogenic effects and the resultant changes in protein expression. Spore suspensions with varying concentrations were prepared for larvicidal bioassays, and protein expressions were analysed using liquid chromatography-mass spectrometry. Subsequently, protein annotation and network analysis were conducted to elucidate infection mechanisms and the proteomic response. Based on the lethal concentrations and time frames, CO exhibited faster larval mortality than BL at lower concentrations. Despite this, both spore types demonstrated comparable overall pathogenic effects. Results from the proteomic profiling revealed 150 proteins with varied expressions following exposure to Ae. albopictus extract, shedding light on distinct infection strategies between the spores. Gene Ontology enrichment and network analysis illustrated the diverse metabolic adaptations of M. anisopliae and interactions with mosquito larvae. This highlighted the complexity of host-pathogen dynamics and the significance of biosynthetic processes, energy storage, and cellular interaction pathways in disease progression. The BL network, consisting 80 proteins and 74 connections, demonstrates the intricate fungal mechanisms triggered by host stimuli. Conversely, the CO network, though smaller, displayed notable interconnectivity and concentrated involvement at the cell periphery, suggesting a deliberate strategy for initial host contact. This study offers valuable insights into proteome dynamics of M. anisopliae's BL and CO for managing mosquito populations and combating disease transmission, thereby significantly advancing public health and environmental conservation efforts.

Genetic modules for α-factor pheromone controlled growth regulation of Saccharomyces cerevisiae

Saccharomyces cerevisiae is a commonly used microorganism in the biotechnological industry. For the industrial heterologous production of compounds, it is of great advantage to work with growth-controllable yeast strains. In our work, we utilized the natural pheromone system of S. cerevisiae and generated a set of different strains possessing an α-pheromone controllable growth behavior. Naturally, the α-factor pheromone is involved in communication between haploid S. cerevisiae cells. Perception of the pheromone initiates several cellular changes, enabling the cells to prepare for an upcoming mating event. We exploited this natural pheromone response system and developed two different plasmid-based modules, in which the target genes, MET15 and FAR1, are under control of the α-factor sensitive FIG1 promoter for a controlled expression in S. cerevisiae. Whereas expression of MET15 led to a growth induction, FAR1 expression inhibited growth. The utilization of low copy number or high copy number plasmids for target gene expression and different concentrations of α-factor allow a finely adjustable control of yeast growth rate.

Engineering a GPCR-based yeast biosensor for a highly sensitive melatonin detection from fermented beverages

Melatonin is a multifunctional molecule with diverse biological roles that holds great value as a health-promoting bioactive molecule in any food product and yeast's ability to produce it has been extensively demonstrated in the last decade. However, its quantification presents costly analytical challenges due to the usual low concentrations found as the result of yeast metabolism. This study addresses these analytical challenges by optimizing a yeast biosensor based on G protein-coupled receptors (GPCR) for melatonin detection and quantitation. Strategic genetic modifications were employed to significantly enhance its sensitivity and fluorescent signal output, making it suitable for detection of yeast-produced melatonin. The optimized biosensor demonstrated significantly improved sensitivity and fluorescence, enabling the screening of 101 yeast strains and the detection of melatonin in various wine samples. This biosensor's efficacy in quantifying melatonin in yeast growth media underscores its utility in exploring melatonin production dynamics and potential applications in functional food development. This study provides a new analytical approach that allows a rapid and cost-effective melatonin analysis to reach deeper insights into the bioactivity of melatonin in fermented products and its implications for human health. These findings highlight the broader potential of biosensor technology in streamlining analytical processes in fermentation science.

Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli

2-Phenylethanol, known for its rose-like odor and antibacterial activity, is synthesized via exogenous phenylpyruvate by the sequential reaction of phenylpyruvate decarboxylase (PDC) and aldehyde reductase. We first targeted ARO10, a phenylpyruvate decarboxylase gene from Saccharomyces cerevisiae, and identified a suitable aldehyde reductase gene. Co-expression of ARO10 and yahK in E. coli transformants yielded 1.1 g/L of 2-phenylethanol in batch culture. We hypothesized that there might be a bottleneck in PDC activity. The computer-based enzyme evolution was utilized to enhance production. The introduction of an amino acid substitution in ARO10 (ARO10 I544W) stabilized the aromatic ring of the phenylpyruvate substrate, increasing 2-phenylethanol yield 4.1-fold compared to wild-type ARO10. Cultivation of ARO10 I544W-expressing E. coli produced 2.5 g/L of 2-phenylethanol with a yield from glucose of 0.16 g/g after 72 h. This approach represents a significant advancement, achieving the highest yield of 2-phenylethanol from glucose using microbes to date.

Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology

Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.

Unravelling bacterial virulence factors in yeast: From identification to the elucidation of their mechanisms of action

Pathogenic bacteria employ virulence factors (VF) to establish infection and cause disease in their host. Yeasts, Saccharomyces cerevisiae and Saccharomyces pombe, are useful model organisms to study the functions of bacterial VFs and their interaction with targeted cellular processes because yeast processes and organelle structures are highly conserved and similar to higher eukaryotes. In this review, we describe the principles and applications of the yeast model for the identification and functional characterisation of bacterial VFs to investigate bacterial pathogenesis. The growth inhibition phenotype caused by the heterologous expression of bacterial VFs in yeast is commonly used to identify candidate VFs. Then, subcellular localisation patterns of bacterial VFs can provide further clues about their target molecules and functions during infection. Yeast knockout and overexpression libraries are also used to investigate VF interactions with conserved eukaryotic cell structures (e.g., cytoskeleton and plasma membrane), and cellular processes (e.g., vesicle trafficking, signalling pathways, and programmed cell death). In addition, the yeast growth inhibition phenotype is also useful for screening new drug leads that target and inhibit bacterial VFs. This review provides an updated overview of new tools, principles and applications to study bacterial VFs in yeast.

The Promising Role of Selenium and Yeast in the Fight Against Protein Amyloidosis

In recent years, increasing attention has been paid to research on diseases related to the deposition of misfolded proteins (amyloids) in various organs. Moreover, modern scientists emphasise the importance of selenium as a bioelement necessary for the proper functioning of living organisms. The inorganic form of selenium-sodium selenite (redox-active)-can prevent the formation of an insoluble polymer in proteins. It is very important to undertake tasks aimed at understanding the mechanisms of action of this element in inhibiting the formation of various types of amyloid. Furthermore, yeast cells play an important role in this matter as a eukaryotic model organism, which is intensively used in molecular research on protein amyloidosis. Due to the lack of appropriate treatment in the general population, the problem of amyloidosis remains unsolved. This extracellular accumulation of amyloid is one of the main factors responsible for the occurrence of Alzheimer's disease. The review presented here contains scientific information discussing a brief description of the possibility of amyloid formation in cells and the use of selenium as a factor preventing the formation of these protein aggregates. Recent studies have shown that the yeast model can be successfully used as a eukaryotic organism in biotechnological research aimed at understanding the essence of the entire amyloidosis process. Understanding the mechanisms that regulate the reaction of yeast to selenium and the phenomenon of amyloidosis is important in the aetiology and pathogenesis of various disease states. Therefore, it is imperative to conduct further research and analysis aimed at explaining and confirming the role of selenium in the processes of protein misfolding disorders. The rest of the article discusses the characteristics of food protein amyloidosis and their use in the food industry. During such tests, their toxicity is checked because not all food proteins can produce amyloid that is toxic to cells. It should also be noted that a moderate diet is beneficial for the corresponding disease relief caused by amyloidosis.

Polydopamine-immobilized yeast cells for portable electrochemical biosensors applied in environmental copper sensing

The coupling of biological organisms with electrodes enables the development of sustainable, low cost, and potentially self-sustained biosensors. A critical aspect is to obtain portable bioelectrodes where the biological material is immobilized on the electrode surface to be utilized on demand. Herein, we developed an approach for the rapid entrapment and immobilization of metabolically active yeast cells in a biocompatible polydopamine layer, which does not require a separate and time-consuming synthesis. The reported approach allows obtaining the "electrical wire" of intact and active yeast cells with resulting current generation from glucose oxidation. Additionally, the electrochemical performance of the biohybrid yeast-based system has been characterized in the presence of CuSO4, a widely used pesticide, in the environmentally relevant concentration range of 20-100 μM. The system enabled the rapid preliminary monitoring of the contaminant based on variations in current generation, with a limit of detection of 12.5 μM CuSO4. The present approach for the facile preparation of portable yeast-based electrochemical biosensors paves the way for the future development of sustainable systems for environmental monitoring.

Elucidation and engineering mitochondrial respiratory-related genes for improving bioethanol production at high temperature in Saccharomyces cerevisiae

Industrial manufacturing of bioproducts, especially bioethanol, can benefit from high-temperature fermentation, which requires the use of thermotolerant yeast strains. Mitochondrial activity in yeast is closely related to its overall metabolism. However, the mitochondrial respiratory changes in response to adaptive thermotolerance are still poorly understood and have been rarely utilized for developing thermotolerant yeast cell factories. Here, adaptive evolution and transcriptional sequencing, as well as whole-genome-level gene knockout, were used to obtain a thermotolerant strain of Saccharomyces cerevisiae. Furthermore, thermotolerance and bioethanol production efficiency of the engineered strain were examined. Physiological evaluation showed the boosted fermentation capacity and suppressed mitochondrial respiratory activity in the thermotolerant strain. The improved fermentation produced an increased supply of adenosine triphosphate required for more active energy-consuming pathways. Transcriptome analysis revealed significant changes in the expression of the genes involved in the mitochondrial respiratory chain. Evaluation of mitochondria-associated gene knockout confirmed that ADK1, DOC1, or MET7 were the key factors for the adaptive evolution of thermotolerance in the engineered yeast strain. Intriguingly, overexpression of DOC1 with TEF1 promoter regulation led to a 10.1% increase in ethanol production at 42 °C. The relationships between thermotolerance, mitochondrial activity, and respiration were explored, and a thermotolerant yeast strain was developed by altering the expression of mitochondrial respiration-related genes. This study provides a better understanding on the physiological mechanism of adaptive evolution of thermotolerance in yeast.

Can biotechnology lead the way toward a sustainable pharmaceutical industry?

The impact-intensive and rapidly growing pharmaceutical industry must ensure its sustainability. This study reveals that environmental sustainability assessments have been conducted for only around 0.2% of pharmaceuticals, environmental impacts have significant variations among the assessed products, and different impact categories have not been consistently studied. Highly varied impacts require assessing more products to understand the industry's sustainability status. Reporting all impact categories will be crucial, especially when comparing production technologies. Biological production of (semi)synthetic pharmaceuticals could reduce their environmental costs, though the high impacts of biologically produced monoclonal antibodies should also be optimized. Considering the sustainability potential of biopharmaceuticals from economic, environmental, and social perspectives, collaboratively guiding their immense market growth would lead to the industry's sustainability transition.

Drug Screening and Validation Targeting TDP-43 Proteinopathy for Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) stands as a rare, yet severely debilitating disorder marked by the deterioration of motor neurons (MNs) within the brain and spinal cord, which is accompanied by degenerated corticobulbar/corticospinal tracts and denervation in skeletal muscles. Despite ongoing research efforts, ALS remains incurable, attributed to its intricate pathogenic mechanisms. A notable feature in the pathology of ALS is the prevalence of TAR DNA-binding protein 43 (TDP-43) proteinopathy, detected in approximately 97% of ALS cases, underscoring its significance in the disease's progression. As a result, strategies targeting the aberrant TDP-43 protein have garnered attention as a potential avenue for ALS therapy. This review delves into the existing drug screening systems aimed at TDP-43 proteinopathy and the models employed for drug efficacy validation. It also explores the hurdles encountered in the quest to develop potent medications against TDP-43 proteinopathy, offering insights into the intricacies of drug discovery and development for ALS. Through this comprehensive analysis, the review sheds light on the critical aspects of identifying and advancing therapeutic solutions for ALS.

Engineering a human P2X2 receptor with altered ligand selectivity in yeast

P2X receptors are a family of ligand gated ion channels found in a range of eukaryotic species including humans but are not naturally present in the yeast Saccharomyces cerevisiae. We demonstrate the first recombinant expression and functional gating of the P2X2 receptor in baker's yeast. We leverage the yeast host for facile genetic screens of mutant P2X2 by performing site saturation mutagenesis at residues of interest, including SNPs implicated in deafness and at residues involved in native binding. Deep mutational analysis and rounds of genetic engineering yield mutant P2X2 F303Y A304W, which has altered ligand selectivity toward the ATP analog AMP-PNP. The F303Y A304W variant shows over 100-fold increased intracellular calcium amplitudes with AMP-PNP compared to the WT receptor and has a much lower desensitization rate. Since AMP-PNP does not naturally activate P2X receptors, the F303Y A304W P2X2 may be a starting point for downstream applications in chemogenetic cellular control. Interestingly, the A304W mutation selectively destabilizes the desensitized state, which may provide a mechanistic basis for receptor opening with suboptimal agonists. The yeast system represents an inexpensive, scalable platform for ion channel characterization and engineering by circumventing the more expensive and time-consuming methodologies involving mammalian hosts.

The yeast-human coevolution: Fungal transition from passengers, colonizers, and invaders

Fungi are the cause of more than a billion infections in humans every year, although their interactions with the host are still neglected compared to bacteria. Major systemic fungal infections are very unusual in the healthy population, due to the long history of coevolution with the human host. Humans are routinely exposed to environmental fungi and can host a commensal mycobiota, which is increasingly considered as a key player in health and disease. Here, we review the current knowledge on host-fungi coevolution and the factors that regulate their interaction. On one hand, fungi have learned to survive and inhabit the host organisms as a natural ecosystem, on the other hand, the host immune system finely tunes the response toward fungi. In turn, recognition of fungi as commensals or pathogens regulates the host immune balance in health and disease. In the human gut ecosystem, yeasts provide a fingerprint of the transient microbiota. Their status as passengers or colonizers is related to the integrity of the gut barrier and the risk of multiple disorders. Thus, the study of this less known component of the microbiota could unravel the rules of the transition from passengers to colonizers and invaders, as well as their dependence on the innate component of the host's immune response. This article is categorized under: Infectious Diseases > Environmental Factors Immune System Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.

Penetrating the ultra-tough yeast cell wall with finite element analysis model-aided design of microtools

Microinjecting yeast cells has been challenging for decades with no significant breakthrough due to the ultra-tough cell wall and low stiffness of the traditional injector tip at the micro-scale. Penetrating this protection wall is the key step for artificially bringing foreign substance into the yeast. In this paper, a yeast cell model was built by using finite element analysis (FEA) method to analyze the penetrating process. The key parameters of the yeast cell wall in the model (the Young's modulus, the shear modulus, and the Lame constant) were calibrated according to a general nanoindentation experiment. Then by employing the calibrated model, the injection parameters were optimized to minimize the cell damage (the maximum cell deformation at the critical stress of the cell wall). Key guidelines were suggested for penetrating the cell wall during microinjection.

Molecular engineering of insulin for recombinant expression in yeast

Since the first administration of insulin to a person with diabetes in 1922, scientific contributions from academia and industry have improved insulin therapy and access. The pharmaceutical need for insulin is now more than 40 tons annually, half of which is produced by recombinant secretory expression in Saccharomyces cerevisiae. We discuss how, in this yeast species, adaptation of insulin precursors by removable structural elements is pivotal for efficient secretory expression. The technologies reviewed have been implemented at industrial scale and are seminal for the supply of human insulin and insulin analogues to people with diabetes now and in the future. Engineering of a target protein with removable structural elements may provide a general approach to yield optimisation.

More than Just Bread and Wine: Using Yeast to Understand Inherited Cytochrome Oxidase Deficiencies in Humans

Inherited defects in cytochrome c oxidase (COX) are associated with a substantial subset of diseases adversely affecting the structure and function of the mitochondrial respiratory chain. This multi-subunit enzyme consists of 14 subunits and numerous cofactors, and it requires the function of some 30 proteins to assemble. COX assembly was first shown to be the primary defect in the majority of COX deficiencies 36 years ago. Over the last three decades, most COX assembly genes have been identified in the yeast Saccharomyces cerevisiae, and studies in yeast have proven instrumental in testing the impact of mutations identified in patients with a specific COX deficiency. The advent of accessible genome-wide sequencing capabilities has led to more patient mutations being identified, with the subsequent identification of several new COX assembly factors. However, the lack of genotype-phenotype correlations and the large number of genes involved in generating a functional COX mean that functional studies must be undertaken to assign a genetic variant as being causal. In this review, we provide a brief overview of the use of yeast as a model system and briefly compare the COX assembly process in yeast and humans. We focus primarily on the studies in yeast that have allowed us to both identify new COX assembly factors and to demonstrate the pathogenicity of a subset of the mutations that have been identified in patients with inherited defects in COX. We conclude with an overview of the areas in which studies in yeast are likely to continue to contribute to progress in understanding disease arising from inherited COX deficiencies.

Stress response and adaptation mechanisms in Kluyveromyces marxianus

Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.

Comb spectroscopy of CO2 produced from microbial metabolism

We have developed a direct frequency comb spectroscopy instrument, which we have tested on Saccharomyces cerevisiae (baker's yeast) by measuring its CO2 output and production rate as we varied the environmental conditions, including the amount and type of feed sugar, the temperature, and the amount of yeast. By feeding isotopically-enhanced sugar to the yeast, we demonstrate the capability of our device to differentiate between two isotopologues of CO2, with a concentration measurement precision of 260 ppm for 12C16O2 and 175 ppm for 13C16O2. We also demonstrate the ability of our spectrometer to measure the proportion of carbon in the feed sugar converted to CO2, and estimate the amount incorporated into the yeast biomass.

POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology

The fission yeast Schizosaccharomyces pombe is a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotations in the PomBase database and genome-wide metabolic models,S. pombe is an attractive option for synthetic biology applications. However,S. pombe currently lacks modular tools for generating genetic circuits with more than 1 transcriptional unit. We developed a toolkit to address this gap. Adapted from the MoClo-YTK plasmid kit for Saccharomyces cerevisiae and using the same modular cloning grammar, our POMBOX toolkit is designed to facilitate fast, efficient, and modular construction of genetic circuits inS. pombe. It allows for interoperability when working with DNA sequences that are functional in bothS. cerevisiae and S. pombe (e.g., protein tags, antibiotic resistance cassettes, and coding sequences). Moreover, POMBOX enables the modular assembly of multigene pathways and increases the possible pathway length from 6 to 12 transcriptional units. We also adapted the stable integration vector homology arms to Golden Gate assembly and tested the genomic integration success rates depending on different sequence sizes, from 4 to 24 kb. We included 14 S. pombe promoters that we characterized using two fluorescent proteins, in both minimally defined (EMM2─Edinburgh minimal media) and complex (YES─yeast extract with supplements) media. Then, we examined the efficacy of 6 S. cerevisiae and 6 synthetic terminators in S. pombe. Finally, we used the POMBOX kit for a synthetic biology application in metabolic engineering and expressed plant enzymes in S. pombe to produce specialized metabolite precursors, namely, methylxanthine, amorpha-4,11-diene, and cinnamic acid from the purine, mevalonate, and aromatic amino acid pathways.

Improving homology-directed repair by small molecule agents for genetic engineering in unconventional yeast?-Learning from the engineering of mammalian systems

The ability to precisely edit genomes by deleting or adding genetic information enables the study of biological functions and the building of efficient cell factories. In many unconventional yeasts, such as those promising new hosts for cell factory design but also human pathogenic yeasts and food spoilers, this progress has been limited by the fact that most yeasts favour non-homologous end joining (NHEJ) over homologous recombination (HR) as a DNA repair mechanism, impairing genetic access to these hosts. In mammalian cells, small molecules that either inhibit proteins involved in NHEJ, enhance protein function in HR, or arrest the cell cycle in HR-dominant phases are regarded as promising agents for the simple and transient increase of HR-mediated genome editing without the need for a priori host engineering. Only a few of these chemicals have been applied to the engineering of yeast, although the targeted proteins are mostly conserved, making chemical agents a yet-underexplored area for enhancing yeast engineering. Here, we consolidate knowledge of the available small molecules that have been used to improve HR efficiency in mammalian cells and the few ones that have been used in yeast. We include available high-throughput-compatible NHEJ/HR quantification assays that could be used to screen for and isolate yeast-specific inhibitors.

Saccharomyces boulardii promoters for control of gene expression in vivo

BACKGROUND

Interest in the use of engineered microbes to deliver therapeutic activities has increased in recent years. The probiotic yeast Saccharomyces boulardii has been investigated for production of therapeutics in the gastrointestinal tract. Well-characterised promoters are a prerequisite for robust therapeutic expression in the gut; however, S. boulardii promoters have not yet been thoroughly characterised in vitro and in vivo.

RESULTS

We present a thorough characterisation of the expression activities of 12 S. boulardii promoters in vitro in glucose, fructose, sucrose, inulin and acetate, under both aerobic and anaerobic conditions, as well as in the murine gastrointestinal tract. Green fluorescent protein was used to report on promoter activity. Promoter expression was found to be carbon-source dependent, with inulin emerging as a favourable carbon source. Furthermore, relative promoter expression in vivo was highly correlated with expression in sucrose (R = 0.99).

CONCLUSIONS

These findings provide insights into S. boulardii promoter activity and aid in promoter selection in future studies utilising S. boulardii to produce therapeutics in the gut.

Comprehensive metabolic profiling of Geotrichum candidum and comparison with Saccharomyces cerevisiae

Geotrichum candidum is a dimorphic yeast used in cheese processing. To our knowledge, no major metabolites have been identified to date in G. candidum except for some amino acid and fatty acid metabolites. This has limited research on the commercial use of G. candidum. In this study, we aimed to analyze temporal changes in the intra- and extra-cellular metabolites of G. candidum and Saccharomyces cerevisiae cultured in YM medium as reference. As a result of metabolite analysis, it was observed that G. candidum tends to accumulate　pentose phosphate pathway compounds, which are involved in nucleic acid synthesis, after 48 h of cultivation when compared to S. cerevisiae. In addition, G. candidum accumulated higher amounts of the antioxidant glutathione in the medium than did S. cerevisiae. In addition, G. candidum accumulated large amounts of B vitamins such as pantothenic acid and nicotinic acid in the medium. Finally, we examined the potential of G. candidum as a host for the production of useful compounds such as pantothenic acid. When cultured in medium supplemented with the pantothenic acid precursor β-alanine, G. candidum produced 12-fold higher amounts of pantothenic acid (30 μM) than that by S. cerevisiae. This study indicates that G. candidum accumulates various useful compounds that are dissimilar to those produced by S. cerevisiae. Furthermore, G. candidum has the potential to produce useful chemicals under appropriate culture conditions.

Beneficial effect of optimizing the expression balance of the mevalonate pathway introduced into the mitochondria on terpenoid production in Saccharomyces cerevisiae

Terpenoids are used in various industries, and Saccharomyces cerevisiae is a promising microorganism for terpenoid production. Introducing the mevalonate (MVA) pathway into the mitochondria of a strain with an augmented inherent cytosolic MVA pathway increased terpenoid production but also led to the accumulation of toxic pyrophosphate intermediates that negatively affected terpenoid production. We first engineered the inherent MVA pathway in the cytosol and then introduced the MVA pathway into the mitochondria using several promoter combinations, considering the toxicity of pyrophosphate intermediates. However, the highest titer, 183 mg/L, tends to be only 5% higher than that of the strain that only augmented the inherent MVA pathway (SYCM1; 174 mg/L). Next, we hypothesized that, in addition to the toxicity of pyrophosphate, other compounds in the MVA pathway could affect the squalene titer. Thus, we constructed a combinatorial strain library expressing MVA pathway enzymes in the mitochondria with various promoter combinations. The highest squalene titer (230 mg/L) was 32% higher than that of SYCM1. The promoter set revealed that mitigation of mono- and pyrophosphate compound accumulation was important for mitochondrial usage. This study demonstrated that a combinatorial strain library is useful for discovering the optimal gene expression balance in engineering yeast.

Open (non-sterile) cultivations of Debaryomyces hansenii for recombinant protein production combining industrial side-streams with high salt content

The halotolerant non-conventional yeast Debaryomyces hansenii can grow in media containing high concentrations of salt (up to 4 M), metabolize alternative carbon sources than glucose, such as lactose or glycerol, and withstand a wide range of temperatures and pH. These inherent capabilities allow this yeast to grow in harsh environments and use alternative feedstock than traditional commercial media. For example, D. hansenii could be a potential cell factory for revalorizing industrial salty by-products, using them as a substrate for producing new valuable bioproducts, boosting a circular economy. In this work, three different salty by-products derived from the dairy and biopharmaceutical industry have been tested as a possible feedstock for D. hansenii's growth. The yeast was not only able to grow efficiently in all of them but also to produce a recombinant protein (Yellow Fluorescent Protein, used as a model) without altering its performance. Moreover, open cultivations at different laboratory scales (1.5 mL and 1 L) were performed under non-sterile conditions and without adding fresh water or any nutritional supplement to the cultivation, making the process cheaper and more sustainable.

High nitrogen concentration causes G2/M arrest in Hanseniaspora vineae

Yeasts have been widely used as a model to better understand cell cycle mechanisms and how nutritional and genetic factors can impact cell cycle progression. While nitrogen scarcity is well known to modulate cell cycle progression, the relevance of nitrogen excess for microorganisms has been overlooked. In our previous work, we observed an absence of proper entry into the quiescent state in Hanseniaspora vineae and identified a potential link between this behavior and nitrogen availability. Furthermore, the Hanseniaspora genus has gained attention due to a significant loss of genes associated with DNA repair and cell cycle. Thus, the aim of our study was to investigate the effects of varying nitrogen concentrations on H. vineae's cell cycle progression. Our findings demonstrated that nitrogen excess, regardless of the source, disrupts cell cycle progression and induces G2/M arrest in H. vineae after reaching the stationary phase. Additionally, we observed a viability decline in H. vineae cells in an ammonium-dependent manner, accompanied by increased production of reactive oxygen species, mitochondrial hyperpolarization, intracellular acidification, and DNA fragmentation. Overall, our study highlights the events of the cell cycle arrest in H. vineae induced by nitrogen excess and attempts to elucidate the possible mechanism triggering this absence of proper entry into the quiescent state.

Rise of synthetic yeast: Charting courses to new applications

Microbes have long provided us with important capabilities, and the genome engineering of microbes has greatly empowered research and applications in biotechnology. This is especially true with the emergence of synthetic biology and recent advances in genome engineering to control microbial behavior. A fully synthetic, rationally designed genome promises opportunities for unprecedented control of cellular function. As a eukaryotic workhorse for research and industrial use, yeast is an organism at the forefront of synthetic biology; the tools and engineered cellular platform being delivered by the Sc2.0 consortium are enabling a new era of bespoke biology. This issue highlights recent advances delivered by this consortium, but hurdles remain to maximize the impact of engineered eukaryotic cells more broadly.

De Novo Biosynthesis of Free Vaccenic Acid with a Low Content of Oleic Acid in Saccharomyces cerevisiae

Omega-7 (ω-7) fatty acids have potential application in the fields of nutraceutical, agricultural, and food industry. The natural ω-7 fatty acids are currently from plants or vegetable oils, which are unsustainable and limited by the availability of plant sources. Here, we developed an innovative biosynthetic route to produce vaccenic acid (C18:1 ω-7) while minimizing oleic acid (C18:1 ω-9) content in Saccharomyces cerevisiae. We have engineered S. cerevisiaeto produce C18:1 ω-7 by expressing a fatty acid elongase from Rattus norvegicus. To reduce the content of C18:1 ω-9, the endogenous desaturase Ole1 was replaced by the desaturase, which has specific activity on palmitoyl-coenzyme A (C16:0-CoA). Finally, the production of free C18:1 ω-7 was improved by optimizing the source of cytochrome b5 and overexpressing endoplasmic reticulum chaperones. After combining these strategies, the yield of C18:1 ω-7 was increased from 0 to 9.3 mg/g DCW and C18:1 ω-9 was decreased from 25.2 mg/g DCW to 1.6 mg/g DCW. This work shows a de novo synthetic pathway to produce the highest amount of free C18:1 ω-7 with a low content of C18:1 ω-9 in S. cerevisiae.

Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning

Quantification of how different environmental cues affect protein allocation can provide important insights for understanding cell physiology. While absolute quantification of proteins can be obtained by resource-intensive mass-spectrometry-based technologies, prediction of protein abundances offers another way to obtain insights into protein allocation. Here we present CAMEL, a framework that couples constraint-based modelling with machine learning to predict protein abundance for any environmental condition. This is achieved by building machine learning models that leverage static features, derived from protein sequences, and condition-dependent features predicted from protein-constrained metabolic models. Our findings demonstrate that CAMEL results in excellent prediction of protein allocation in E. coli (average Pearson correlation of at least 0.9), and moderate performance in S. cerevisiae (average Pearson correlation of at least 0.5). Therefore, CAMEL outperformed contending approaches without using molecular read-outs from unseen conditions and provides a valuable tool for using protein allocation in biotechnological applications.

Molecularly Imprinted Polymers Using Yeast as a Supporting Substrate

Molecularly imprinted polymers (MIPs) have gained significant attention as artificial receptors due to their low cost, mild operating conditions, and excellent selectivity. To optimize the synthesis process and enhance the recognition performance, various support materials for molecular imprinting have been explored as a crucial research direction. Yeast, a biological material, offers advantages such as being green and environmentally friendly, low cost, and easy availability, making it a promising supporting substrate in the molecular imprinting process. We focus on the preparation of different types of MIPs involving yeast and elaborate on the specific roles it plays in each case. Additionally, we discuss the advantages and limitations of yeast in the preparation of MIPs and conclude with the challenges and future development trends of yeast in molecular imprinting research.

Cellular Stress Impact on Yeast Activity in Biotechnological Processes-A Short Overview

The importance of Saccharomyces cerevisiae yeast cells is known worldwide, as they are the most used microorganisms in biotechnology for bioethanol and biofuel production. Also, they are analyzed and studied for their similar internal biochemical processes to human cells, for a better understanding of cell aging and response to cell stressors. The special ability of S. cerevisiae cells to develop in both aerobic and anaerobic conditions makes this microorganism a viable model to study the transformations and the way in which cellular metabolism is directed to face the stress conditions due to environmental changes. Thus, this review will emphasize the effects of oxidative, ethanol, and osmotic stress and also the physiological and genetic response of stress mitigation in yeast cells.

Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony

Intracellular fluxes represent a joint outcome of cellular transcription and translation and reflect the availability and usage of nutrients from the environment. While approaches from the constraint-based metabolic framework can accurately predict cellular phenotypes, such as growth and exchange rates with the environment, accurate prediction of intracellular fluxes remains a pressing problem. Parsimonious flux balance analysis (pFBA) has become an approach of choice to predict intracellular fluxes by employing the principle of efficient usage of protein resources. Nevertheless, comparative analyses of intracellular flux predictions from pFBA against fluxes estimated from labeling experiments remain scarce. Here, we posited that steady-state flux distributions derived from the principle of maximizing multi-reaction dependencies are of improved accuracy and precision than those resulting from pFBA. To this end, we designed a constraint-based approach, termed complex-balanced FBA (cbFBA), to predict steady-state flux distributions that support the given specific growth rate and exchange fluxes. We showed that the steady-state flux distributions resulting from cbFBA in comparison to pFBA show better agreement with experimentally measured fluxes from 17 Escherichia coli strains and are more precise, due to the smaller space of alternative solutions. We also showed that the same principle holds in eukaryotes by comparing the predictions of pFBA and cbFBA against experimentally derived steady-state flux distributions from 26 knock-out mutants of Saccharomyces cerevisiae. Furthermore, our results showed that intracellular fluxes predicted by cbFBA provide better support for the principle of minimizing metabolic adjustment between mutants and wild types. Together, our findings point that other principles that consider the dynamics and coordination of steady states may govern the distribution of intracellular fluxes.

Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense

Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.

Modelling the Tumour Microenvironment, but What Exactly Do We Mean by "Model"?

The Oxford English Dictionary includes 17 definitions for the word "model" as a noun and another 11 as a verb. Therefore, context is necessary to understand the meaning of the word model. For instance, "model railways" refer to replicas of railways and trains at a smaller scale and a "model student" refers to an exemplary individual. In some cases, a specific context, like cancer research, may not be sufficient to provide one specific meaning for model. Even if the context is narrowed, specifically, to research related to the tumour microenvironment, "model" can be understood in a wide variety of ways, from an animal model to a mathematical expression. This paper presents a review of different "models" of the tumour microenvironment, as grouped by different definitions of the word into four categories: model organisms, in vitro models, mathematical models and computational models. Then, the frequencies of different meanings of the word "model" related to the tumour microenvironment are measured from numbers of entries in the MEDLINE database of the United States National Library of Medicine at the National Institutes of Health. The frequencies of the main components of the microenvironment and the organ-related cancers modelled are also assessed quantitatively with specific keywords. Whilst animal models, particularly xenografts and mouse models, are the most commonly used "models", the number of these entries has been slowly decreasing. Mathematical models, as well as prognostic and risk models, follow in frequency, and these have been growing in use.

New Insights on the Uptake and Trafficking of Coenzyme Q

Coenzyme Q (CoQ) is an essential lipid with many cellular functions, such as electron transport for cellular respiration, antioxidant protection, redox homeostasis, and ferroptosis suppression. Deficiencies in CoQ due to aging, genetic disease, or medication can be ameliorated by high-dose supplementation. As such, an understanding of the uptake and transport of CoQ may inform methods of clinical use and identify how to better treat deficiency. Here, we review what is known about the cellular uptake and intracellular distribution of CoQ from yeast, mammalian cell culture, and rodent models, as well as its absorption at the organism level. We discuss the use of these model organisms to probe the mechanisms of uptake and distribution. The literature indicates that CoQ uptake and distribution are multifaceted processes likely to have redundancies in its transport, utilizing the endomembrane system and newly identified proteins that function as lipid transporters. Impairment of the trafficking of either endogenous or exogenous CoQ exerts profound effects on metabolism and stress response. This review also highlights significant gaps in our knowledge of how CoQ is distributed within the cell and suggests future directions of research to better understand this process.

A landing pad system for multicopy gene integration in Issatchenkia orientalis

The robust nature of the non-conventional yeast Issatchenkia orientalis allows it to grow under highly acidic conditions and therefore, has gained increasing interest in producing organic acids using a variety of carbon sources. Recently, the development of a genetic toolbox for I. orientalis, including an episomal plasmid, characterization of multiple promoters and terminators, and CRISPR-Cas9 tools, has eased the metabolic engineering efforts in I. orientalis. However, multiplex engineering is still hampered by the lack of efficient multicopy integration tools. To facilitate the construction of large, complex metabolic pathways by multiplex CRISPR-Cas9-mediated genome editing, we developed a bioinformatics pipeline to identify and prioritize genome-wide intergenic loci and characterized 47 gRNAs located in 21 intergenic regions. These loci are screened for guide RNA cutting efficiency, integration efficiency of a gene cassette, the resulting cellular fitness, and GFP expression level. We further developed a landing pad system using components from these well-characterized loci, which can aid in the integration of multiple genes using single guide RNA and multiple repair templates of the user's choice. We have demonstrated the use of the landing pad for simultaneous integrations of 2, 3, 4, or 5 genes to the target loci with efficiencies greater than 80%. As a proof of concept, we showed how the production of 5-aminolevulinic acid can be improved by integrating five copies of genes at multiple sites in one step. We have further demonstrated the efficiency of this tool by constructing a metabolic pathway for succinic acid production by integrating five gene expression cassettes using a single guide RNA along with five different repair templates, leading to the production of 9 g/L of succinic acid in batch fermentations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in a non-conventional yeast. This landing pad system will be a valuable tool for the metabolic engineering of I. orientalis.

Recent progress in fucosylated derivatives of lacto-N-tetraose and lacto-N-neotetraose

Human milk oligosaccharides (HMOs) have attracted considerable attention owing to their unique physiological functions. Two important tetrasaccharides, lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), are core structures of HMOs. Their safety has been evaluated and they can be added to infant formula as functional ingredients. The fucosylated derivatives of LNT and LNnT, mainly lacto-N-fucopentaose (LNFP) I, LNFP II, LNFP III, and lacto-N-difucohexaose I, exhibit prominent physiological characteristics, including modificating the intestinal microbiota, immunomodulation, anti-bacterial activities, and antiviral infection. However, they have received lesser attention than 2'-fucosyllactose. As precursors, LNT and LNnT are connected to one or two fucosyl units through α1,2/3/4 glycosidic bonds, forming a series of compounds with complex structures. These complex fucosylated oligosaccharides can be biologically synthesized using enzymatic and cell factory approaches. This review summarizes the occurrence, physiological effects, and biosynthesis of fucosylated LNT and LNnT derivatives and their future development.

Enhancement of β-Caryophyllene Biosynthesis in Saccharomyces cerevisiae via Synergistic Evolution of β-Caryophyllene Synthase and Engineering the Chassis

β-Caryophyllene is a plant-derived bicyclic sesquiterpene with multiple biological functions. β-Caryophyllene production by engineered Saccharomyces cerevisiae represents a promising technological route. However, the low catalytic activity of β-caryophyllene synthase (CPS) is one of the main restrictive factors for β-caryophyllene production. Here, directed evolution of the Artemisia annua CPS was performed, and variants of CPS enhancing the β-caryophyllene biosynthesis in S. cerevisiae were obtained, in which an E353D mutant enzyme presented large improvements in Vmax and Kcat. The Kcat/Km of the E353D mutant was 35.5% higher than that of wild-type CPS. Moreover, the E353D variant exhibited higher catalytic activity in much wider pH and temperature ranges. Thus, both the higher catalytic activity and the robustness of the E353D variant contribute to the 73.3% increase in β-caryophyllene production. Furthermore, the S. cerevisiae chassis was engineered by overexpressing genes related to β-alanine metabolism and MVA pathway to enhance the synthesis of the precursor, and ATP-binding cassette transporter gene variant STE6T1025N to improve the transmembrane transport of β-caryophyllene. The combined engineering of CPS and chassis resulted in 70.45 mg/L of β-caryophyllene after 48 h of cultivation in a test tube, which was 2.93-fold of that of the original strain. Finally, a β-caryophyllene yield of 594.05 mg/L was obtained by fed-batch fermentation, indicating the potential of β-caryophyllene production by yeast.

Phosphoinositide and redox dysregulation by the anticancer methylthioadenosine phosphorylase transition state inhibitor

Methylthio-DADMe-immucillin-A (MTDIA) is an 86 picomolar inhibitor of 5'-methylthioadenosine phosphorylase (MTAP) with potent and specific anti-cancer efficacy. MTAP salvages S-adenosylmethionine (SAM) from 5'-methylthioadenosine (MTA), a toxic metabolite produced during polyamine biosynthesis. Changes in MTAP expression are implicated in cancer growth and development, making MTAP an appealing target for anti-cancer therapeutics. Since SAM is involved in lipid metabolism, we hypothesised that MTDIA alters the lipidomes of MTDIA-treated cells. To identify these effects, we analysed the lipid profiles of MTDIA-treated Saccharomyces cerevisiae using ultra-high resolution accurate mass spectrometry (UHRAMS). MTAP inhibition by MTDIA, and knockout of the Meu1 gene that encodes for MTAP in yeast, caused global lipidomic changes and differential abundance of lipids involved in cell signaling. The phosphoinositide kinase/phosphatase signaling network was specifically impaired upon MTDIA treatment, and was independently validated and further characterised via altered localization of proteins integral to this network. Functional consequences of dysregulated lipid metabolism included a decrease in reactive oxygen species (ROS) levels induced by MTDIA that was contemporaneous with changes in immunological response factors (nitric oxide, tumour necrosis factor-alpha and interleukin-10) in mammalian cells. These results indicate that lipid homeostasis alterations and concomitant downstream effects may be associated with MTDIA mechanistic efficacy.

High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics

Identifying metabolites in model organisms is critical for many areas of biology, including unravelling disease aetiology or elucidating functions of putative enzymes. Even now, hundreds of predicted metabolic genes in Saccharomyces cerevisiae remain uncharacterized, indicating that our understanding of metabolism is far from complete even in well-characterized organisms. While untargeted high-resolution mass spectrometry (HRMS) enables the detection of thousands of features per analysis, many of these have a non-biological origin. Stable isotope labelling (SIL) approaches can serve as credentialing strategies to distinguish biologically relevant features from background signals, but implementing these experiments at large scale remains challenging. Here, we developed a SIL-based approach for high-throughput untargeted metabolomics in S. cerevisiae, including deep-48 well format-based cultivation and metabolite extraction, building on the peak annotation and verification engine (PAVE) tool. Aqueous and nonpolar extracts were analysed using HILIC and RP liquid chromatography, respectively, coupled to Orbitrap Q Exactive HF mass spectrometry. Of the approximately 37,000 total detected features, only 3-7% of the features were credentialed and used for data analysis with open-source software such as MS-DIAL, MetFrag, Shinyscreen, SIRIUS CSI:FingerID, and MetaboAnalyst, leading to the successful annotation of 198 metabolites using MS² database matching. Comparable metabolic profiles were observed for wild-type and sdh1Δ yeast strains grown in deep-48 well plates versus the classical shake flask format, including the expected increase in intracellular succinate concentration in the sdh1Δ strain. The described approach enables high-throughput yeast cultivation and credentialing-based untargeted metabolomics, providing a means to efficiently perform molecular phenotypic screens and help complete metabolic networks.

Cross-species microbial genome transfer: a Review

Synthetic biology combines the disciplines of biology, chemistry, information science, and engineering, and has multiple applications in biomedicine, bioenergy, environmental studies, and other fields. Synthetic genomics is an important area of synthetic biology, and mainly includes genome design, synthesis, assembly, and transfer. Genome transfer technology has played an enormous role in the development of synthetic genomics, allowing the transfer of natural or synthetic genomes into cellular environments where the genome can be easily modified. A more comprehensive understanding of genome transfer technology can help to extend its applications to other microorganisms. Here, we summarize the three host platforms for microbial genome transfer, review the recent advances that have been made in genome transfer technology, and discuss the obstacles and prospects for the development of genome transfer.

RNAi-mediated mortality of Culex quinquefasciatus using two delivery methods of potential field application

With increasing reports of resistance to traditional insecticides, there is a need for innovative ways for mosquito control. RNAi is a sequence-specific molecular biology technique for gene silencing through degradation of mRNA and prevention of protein translation. Some genes are essential for insect life and their silencing can lead to insect morbidity and/or mortality. Searching for lethal genes in Culex quinquefasciatus, we found dynamin, ROP, HMGR and JHAMT to be lethal targets for RNAi in initial screening through larval soaking in dsRNA solution. Two delivery methods, chitosan nanoparticles and genetically modified yeast cells, were used in this study and proved effective in inducing high larval mortality and low adult emergence. Adult emergence after chitosan nanoparticles/dsRNA treatment was 12.67% ± 1.76 (HMGR), 17.33% ± 1.76 (dynamin), 18.67% ± 0.67 (ROP), and 35.33% ± 0.67 (JHAMT). Genetically modified yeast increased mortalities as adult emergence was 8.33% ± 1.67 (HMGR), 13.33% ± 3.33 (dynamin), and 10% ± 2.89 (JHAMT and ROP). Chitosan nanoparticles retained 75% of its biological activity whereas yeast cells retained >95% of their activities after 7 days of incubation in water. In conclusion, our results showed that these four genes are good targets for C. quinquefasciatus control using RNAi packaged in either chitosan nanoparticles or genetically modified yeast cells.

Tumor heterogeneity: preclinical models, emerging technologies, and future applications

Heterogeneity describes the differences among cancer cells within and between tumors. It refers to cancer cells describing variations in morphology, transcriptional profiles, metabolism, and metastatic potential. More recently, the field has included the characterization of the tumor immune microenvironment and the depiction of the dynamics underlying the cellular interactions promoting the tumor ecosystem evolution. Heterogeneity has been found in most tumors representing one of the most challenging behaviors in cancer ecosystems. As one of the critical factors impairing the long-term efficacy of solid tumor therapy, heterogeneity leads to tumor resistance, more aggressive metastasizing, and recurrence. We review the role of the main models and the emerging single-cell and spatial genomic technologies in our understanding of tumor heterogeneity, its contribution to lethal cancer outcomes, and the physiological challenges to consider in designing cancer therapies. We highlight how tumor cells dynamically evolve because of the interactions within the tumor immune microenvironment and how to leverage this to unleash immune recognition through immunotherapy. A multidisciplinary approach grounded in novel bioinformatic and computational tools will allow reaching the integrated, multilayered knowledge of tumor heterogeneity required to implement personalized, more efficient therapies urgently required for cancer patients.