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Methods in Molecular Biology (Clifton,... 2015The method of displaying recombinant proteins on the surface of Saccharomyces cerevisiae via genetic fusion to an abundant cell wall protein, a technology known as yeast... (Review)
Review
The method of displaying recombinant proteins on the surface of Saccharomyces cerevisiae via genetic fusion to an abundant cell wall protein, a technology known as yeast surface display, or simply, yeast display, has become a valuable protein engineering tool for a broad spectrum of biotechnology and biomedical applications. This review focuses on the use of yeast display for engineering protein affinity, stability, and enzymatic activity. Strategies and examples for each protein engineering goal are discussed. Additional applications of yeast display are also briefly presented, including protein epitope mapping, identification of protein-protein interactions, and uses of displayed proteins in industry and medicine.
Topics: Cell Surface Display Techniques; Epitope Mapping; Protein Binding; Protein Engineering; Protein Stability; Recombinant Proteins; Saccharomyces cerevisiae
PubMed: 26060074
DOI: 10.1007/978-1-4939-2748-7_8 -
FEMS Yeast Research Feb 2022Yeasts have been widely used for production of bread, beer and wine, as well as for production of bioethanol, but they have also been designed as cell factories to... (Review)
Review
Yeasts have been widely used for production of bread, beer and wine, as well as for production of bioethanol, but they have also been designed as cell factories to produce various chemicals, advanced biofuels and recombinant proteins. To systematically understand and rationally engineer yeast metabolism, genome-scale metabolic models (GEMs) have been reconstructed for the model yeast Saccharomyces cerevisiae and nonconventional yeasts. Here, we review the historical development of yeast GEMs together with their recent applications, including metabolic flux prediction, cell factory design, culture condition optimization and multi-yeast comparative analysis. Furthermore, we present an emerging effort, namely the integration of proteome constraints into yeast GEMs, resulting in models with improved performance. At last, we discuss challenges and perspectives on the development of yeast GEMs and the integration of proteome constraints.
Topics: Biofuels; Metabolic Engineering; Proteome; Retrospective Studies; Saccharomyces cerevisiae
PubMed: 35094064
DOI: 10.1093/femsyr/foac003 -
FEMS Yeast Research Sep 2018In the search for interventions against aging and age-related diseases, biological screening platforms are indispensable tools to identify anti-aging compounds among... (Review)
Review
In the search for interventions against aging and age-related diseases, biological screening platforms are indispensable tools to identify anti-aging compounds among large substance libraries. The budding yeast, Saccharomyces cerevisiae, has emerged as a powerful chemical and genetic screening platform, as it combines a rapid workflow with experimental amenability and the availability of a wide range of genetic mutant libraries. Given the amount of conserved genes and aging mechanisms between yeast and human, testing candidate anti-aging substances in yeast gene-deletion or overexpression collections, or de novo derived mutants, has proven highly successful in finding potential molecular targets. Yeast-based studies, for example, have led to the discovery of the polyphenol resveratrol and the natural polyamine spermidine as potential anti-aging agents. Here, we present strategies for pharmacological anti-aging screens in yeast, discuss common pitfalls and summarize studies that have used yeast for drug discovery and target identification.
Topics: Aging; Drug Discovery; Gene Library; Genetic Testing; Humans; Microbial Viability; Models, Biological; Phenotype; Saccharomyces cerevisiae; Small Molecule Libraries
PubMed: 29905792
DOI: 10.1093/femsyr/foy020 -
Current Opinion in Chemical Biology Feb 2019Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will... (Review)
Review
Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will therefore enhance our understanding of cellular function. Here we review recent developments in this field with regard to mass spectrometry, fluorescence microscopy and computational prediction methods. We highlight relative strengths and limitations of current methodologies focussing particularly on studies in the yeast Saccharomyces cerevisiae. We further present the first cell-wide spatial proteome map of S. cerevisiae, generated using hyperLOPIT, a mass spectrometry-based protein correlation profiling technique. We compare protein subcellular localisation assignments from this map, with two published fluorescence microscopy studies and show that confidence in localisation assignment is attained using multiple orthogonal methods that provide complementary data.
Topics: Mass Spectrometry; Microscopy, Fluorescence; Proteomics; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 30503867
DOI: 10.1016/j.cbpa.2018.10.026 -
Biosensors May 2020Biosensors are regarded as a powerful tool to detect and monitor environmental contaminants, toxins, and, more generally, organic or chemical markers of potential... (Review)
Review
Biosensors are regarded as a powerful tool to detect and monitor environmental contaminants, toxins, and, more generally, organic or chemical markers of potential threats to human health. They are basically composed of a sensor part made up of either live cells or biological active molecules coupled to a transducer/reporter technological element. Whole-cells biosensors may be based on animal tissues, bacteria, or eukaryotic microorganisms such as yeasts and microalgae. Although very resistant to adverse environmental conditions, yeasts can sense and respond to a wide variety of stimuli. As eukaryotes, they also constitute excellent cellular models to detect chemicals and organic contaminants that are harmful to animals. For these reasons, combined with their ease of culture and genetic modification, yeasts have been commonly used as biological elements of biosensors since the 1970s. This review aims first at giving a survey on the different types of yeast-based biosensors developed for the environmental and medical domains. We then present the technological developments currently undertaken by academic and corporate scientists to further drive yeasts biosensors into a new era where the biological element is optimized in a tailor-made fashion by in silico design and where the output signals can be recorded or followed on a smartphone.
Topics: Animals; Biosensing Techniques; Humans; Saccharomyces cerevisiae; Smartphone
PubMed: 32413968
DOI: 10.3390/bios10050051 -
FEMS Yeast Research Feb 2020Wine is an archetypal traditional fermented beverage with strong territorial and socio-cultural connotations. Its 7000 year history is patterned by a tradition of... (Review)
Review
Wine is an archetypal traditional fermented beverage with strong territorial and socio-cultural connotations. Its 7000 year history is patterned by a tradition of innovation. Every value-adding innovation - whether in the vineyard, winery, supply chain or marketplace - that led to the invention of a new tradition spurred progress and created a brighter future from past developments. In a way, wine traditions can be defined as remembered innovations from the distant past - inherited knowledge and wisdom that withstood the test of time. Therefore, it should not be assumed a priori that tradition and innovation are polar opposites. The relations between the forces driven by the anchors of tradition and the wings of innovation do not necessarily involve displacement, conflict or exclusiveness. Innovation can strengthen wine tradition, and the reinvention of a tradition-bound practice, approach or concept can foster innovation. In cases where a paradigm-shifting innovation disrupts a tradition, the process of such an innovation transitioning into a radically new tradition can become protracted while proponents of divergent opinions duke it out. Sometimes these conflicting opinions are based on fact, and sometimes not. The imperfections of such a debate between the 'ancients' and the 'moderns' can, from time to time, obscure the line between myth and reality. Therefore, finding the right balance between traditions worth keeping and innovations worth implementing can be complex. The intent here is to harness the creative tension between science fiction and science fact when innovation's first-principles challenge the status quo by re-examining the foundational principles about a core traditional concept, such as terroir. Poignant questions are raised about the importance of the terroir (biogeography) of yeasts and the value of the microbiome of grapes to wine quality. This article imagines a metaphorical terroir free from cognitive biases where diverse perspectives can converge to uncork the effervescent power of territorial yeast populations as well as 'nomadic' yeast starter cultures. At the same time, this paper also engages in mental time-travel. A future scenario is imagined, explored, tested and debated where terroir-less yeast avatars are equipped with designer genomes to safely and consistently produce, individually or in combination with region-specific wild yeasts and or other starter cultures, high-quality wine according to the preferences of consumers in a range of markets. The purpose of this review is to look beyond the horizon and to synthesize a link between what we know now and what could be. This article informs readers where to look without suggesting what they must see as a way forward. In the context of one of the world's oldest fermentation industries - steeped in a rich history of tradition and innovation - the mantra here is: respect the past, lead the present and secure the future of wine.
Topics: Biodiversity; Fermentation; Food Microbiology; Microbiota; Saccharomyces cerevisiae; Vitis; Wine
PubMed: 31830254
DOI: 10.1093/femsyr/foz084 -
Biochimica Et Biophysica Acta.... Jan 2020The turnover of phospholipids plays an essential role in membrane lipid homeostasis by impacting both lipid head group and acyl chain composition. This review focusses... (Review)
Review
The turnover of phospholipids plays an essential role in membrane lipid homeostasis by impacting both lipid head group and acyl chain composition. This review focusses on the degradation and acyl chain remodeling of the major phospholipid classes present in the ER membrane of the reference eukaryote Saccharomyces cerevisiae, i.e. phosphatidylcholine (PC), phosphatidylinositol (PI) and phosphatidylethanolamine (PE). Phospholipid turnover reactions are introduced, and the occurrence and important functions of phospholipid remodeling in higher eukaryotes are briefly summarized. After presenting an inventory of established mechanisms of phospholipid acyl chain exchange, current knowledge of phospholipid degradation and remodeling by phospholipases and acyltransferases localized to the yeast ER is summarized. PC is subject to the PC deacylation-reacylation remodeling pathway (PC-DRP) involving a phospholipase B, the recently identified glycerophosphocholine acyltransferase Gpc1p, and the broad specificity acyltransferase Ale1p. PI is post-synthetically enriched in C18:0 acyl chains by remodeling reactions involving Cst26p. PE may undergo turnover by the phospholipid: diacylglycerol acyltransferase Lro1p as first step in acyl chain remodeling. Clues as to the functions of phospholipid acyl chain remodeling are discussed.
Topics: Acylation; Animals; Endoplasmic Reticulum; Humans; Phosphatidylcholines; Phosphatidylethanolamines; Phosphatidylinositols; Phospholipids; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 31146038
DOI: 10.1016/j.bbalip.2019.05.006 -
Chemistry and Physics of Lipids Jan 2014Sphingolipids are recognized as signaling mediators in a growing number of pathways, and represent potential targets to address many diseases. The study of sphingolipid... (Review)
Review
Sphingolipids are recognized as signaling mediators in a growing number of pathways, and represent potential targets to address many diseases. The study of sphingolipid signaling in yeast has created a number of breakthroughs in the field, and has the potential to lead future advances. The aim of this article is to provide an inclusive view of two major frontiers in yeast sphingolipid signaling. In the first section, several key studies in the field of sphingolipidomics are consolidated to create a yeast sphingolipidome that ranks nearly all known sphingolipid species by their level in a resting yeast cell. The second section presents an overview of most known phenotypes identified for sphingolipid gene mutants, presented with the intention of illuminating not yet discovered connections outside and inside of the field.
Topics: Humans; Phenotype; Saccharomyces cerevisiae; Signal Transduction; Sphingolipids
PubMed: 24220500
DOI: 10.1016/j.chemphyslip.2013.10.006 -
Bioengineered Dec 2021Oral vaccine and gene delivery systems must be engineered to withstand several different physiological environments, such as those present in the oral cavity, stomach,... (Review)
Review
Oral vaccine and gene delivery systems must be engineered to withstand several different physiological environments, such as those present in the oral cavity, stomach, and jejunum, each of which exhibits varying pH levels and enzyme distributions. Additionally, these systems must be designed to ensure appropriate gastrointestinal absorption and tissue/cellular targeting properties. Yeasts-based delivery vehicles are excellent candidates for oral vaccine and oral gene therapies as many species possess cellular characteristics resulting in enhanced resistance to the harsh gastrointestinal (GI) environment and facilitated passage across the mucosal barrier. Yeast capsules can stimulate and modulate host immune responses, which is beneficial for vaccine efficacy. In addition, recombinant modification of yeasts to express cell penetrating proteins and injection mechanisms along with efficient cell adhering capabilities can potentially improve transfection rates of genetic material. In this literature review, we present evidence supporting the beneficial role yeast-based delivery systems can play in increasing the efficacy of oral administration of vaccines and gene therapies.
Topics: Administration, Oral; Animals; Drug Delivery Systems; Humans; Nanostructures; Saccharomyces cerevisiae; Vaccines
PubMed: 34592900
DOI: 10.1080/21655979.2021.1985816 -
FEMS Yeast Research Nov 2016The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry.... (Review)
Review
The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype-environment-phenotype relationships.
Topics: Adaptation, Biological; Metabolic Networks and Pathways; Microbial Interactions; Saccharomyces cerevisiae
PubMed: 27634775
DOI: 10.1093/femsyr/fow080