Life with 6000 genes

Recombinant Protein Technology in the Challenging Era of Coronaviruses

Coronaviruses have caused devastation in both human and animal populations, affecting both health and the economy. Amidst the emergence and re-emergence of coronaviruses, humans need to surmount the health and economic threat of coronaviruses through science and evidence-based approaches. One of these approaches is through biotechnology, particularly the heterologous production of biopharmaceutical proteins. This review article briefly describes the genome, general virion morphology, and key structural proteins of different coronaviruses affecting animals and humans. In addition, this review paper also presents the different systems in recombinant protein technology such as bacteria, yeasts, plants, mammalian cells, and insect/insect cells systems used to express key structural proteins in the development of countermeasures such as diagnostics, prophylaxis, and therapeutics in the challenging era of coronaviruses.

Interactions between Core Elements of the Botrytis cinerea Circadian Clock Are Modulated by Light and Different Protein Domains

Botrytis cinerea possesses a complex light-sensing system composed of eleven photoreceptors. In B. cinerea, bcwcl1 encodes for the BcWCL1 protein, the orthologue of the blue-light photoreceptor WC-1 from Neurospora crassa. The functional partner of BcWCL1 is the BcWCL2 protein, both interacting in the nucleus and forming the B. cinerea white collar complex (BcWCC). This complex is required for photomorphogenesis and circadian regulation. However, no molecular evidence shows a light-dependent interaction between the BcWCC components or light-sensing capabilities in BcWCL1. In this work, by employing a yeast two-hybrid system that allows for the in vivo analysis of protein-protein interactions, we confirm that BcWCL1 and BcWCL2 interact in the absence of light as well as upon blue-light stimulation, primarily through their PAS (Per-Arnt-Sim) domains. Deletion of the PAS domains present in BcWCL1 (BcWCL1PAS∆) or BcWCL2 (BcWCL2PAS∆) severely impairs the interaction between these proteins. Interestingly, the BcWCL1PAS∆ protein shows a blue-light response and interacts with BcWCL2 or BcWCL2PAS∆ upon light stimulation. Finally, we demonstrate that BcWCL1 and BcWCL1PAS∆ respond to blue light by introducing a point mutation in the photoactive cysteine, confirming that both proteins are capable of light sensing. Altogether, the results revealed the complexity of protein-protein interactions occurring between the core elements of the B. cinerea circadian clock.

Gradients in gene essentiality reshape antibacterial research

Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.

An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function

The evolutionary rates of functionally related genes often covary. We present a gene coevolution network inferred from examining nearly 3 million orthologous gene pairs from 332 budding yeast species spanning ~400 million years of evolution. Network modules provide insight into cellular and genomic structure and function. Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker's yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity. Mapping the network onto the chromosomes of S. cerevisiae and Candida albicans revealed that coevolving orthologous genes are not physically clustered in either species; rather, they are often located on different chromosomes or far apart on the same chromosome. The coevolution network captures the hierarchy of cellular structure and function, provides a roadmap for genotype-to-phenotype discovery, and portrays the genome as a linked ensemble of genes.

High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing

During the last two decades, whole-genome sequencing has revolutionized genetic research in all kingdoms, including fungi. More than 1000 fungal genomes have been submitted to sequence databases, mostly obtained through second generation short-read DNA sequencing. As a result, highly fragmented genome drafts have typically been obtained. However, with the emergence of third generation long-read DNA sequencing, the assembly challenge can be overcome and highly contiguous assemblies obtained. Such attractive results, however, are extremely dependent on the ability to extract highly purified high molecular weight (HMW) DNA. Extraction of such DNA is currently a significant challenge for all species with cell walls, not least fungi. In this study, four isolates of filamentous ascomycetes (Apiospora pterospermum, Aspergillus sp. (subgen. Cremei), Aspergillus westerdijkiae, and Penicillium aurantiogriseum) were used to develop extraction and purification methods that result in HMW DNA suitable for third generation sequencing. We have tested and propose two straightforward extraction methods based on treatment with either a commercial kit or traditional phenol-chloroform extraction both in combination with a single commercial purification method that result in high quality HMW DNA from filamentous ascomycetes. Our results demonstrated that using these DNA extraction methods and coverage, above 75 x of our haploid filamentous ascomycete fungal genomes result in complete and contiguous assemblies.

Differential Gene Expression of Mucor lusitanicus under Aerobic and Anaerobic Conditions

Mucor lusitanicus and some other members of the fungal order Mucorales display the phenomenon of morphological dimorphism. This means that these fungi aerobically produce filamentous hyphae, developing a coenocytic mycelium, but they grow in a multipolar yeast-like form under anaerobiosis. Revealing the molecular mechanism of the reversible yeast-hyphal transition can be interesting for both the biotechnological application and in the understanding of the pathomechanism of mucormycosis. In the present study, transcriptomic analyses were carried out after cultivating the fungus either aerobically or anaerobically revealing significant changes in gene expression under the two conditions. In total, 539 differentially expressed genes (FDR < 0.05, |log2FC| ≥ 3) were identified, including 190 upregulated and 349 downregulated transcripts. Within the metabolism-related genes, carbohydrate metabolism was proven to be especially affected. Anaerobiosis also affected the transcription of transporters: among the 14 up- and 42 downregulated transporters, several putative sugar transporters were detected. Moreover, a considerable number of transcripts related to amino acid transport and metabolism, lipid transport and metabolism, and energy production and conversion were proven to be downregulated when the culture had been transferred into an anaerobic atmosphere.

A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase

Despite decades of research and the availability of the full genomic sequence of the baker's yeast Saccharomyces cerevisiae, still a large fraction of its genome is not functionally annotated. This hinders our ability to fully understand cellular activity and suggests that many additional processes await discovery. The recent years have shown an explosion of high-quality genomic and structural data from multiple organisms, ranging from bacteria to mammals. New computational methods now allow us to integrate these data and extract meaningful insights into the functional identity of uncharacterized proteins in yeast. Here, we created a database of sensitive sequence similarity predictions for all yeast proteins. We use this information to identify candidate enzymes for known biochemical reactions whose enzymes are unidentified, and show how this provides a powerful basis for experimental validation. Using one pathway as a test case we pair a new function for the previously uncharacterized enzyme Yhr202w, as an extra-cellular AMP hydrolase in the NAD degradation pathway. Yhr202w, which we now term Smn1 for Scavenger MonoNucleotidase 1, is a highly conserved protein that is similar to the human protein E5NT/CD73, which is associated with multiple cancers. Hence, our new methodology provides a paradigm, that can be adopted to other organisms, for uncovering new enzymatic functions of uncharacterized proteins.

New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.

Beyond Mendelian Inheritance: Genetic Buffering and Phenotype Variability

Understanding the way genes work amongst individuals and across generations to shape form and function is a common theme for many genetic studies. The recent advances in genetics, genome engineering and DNA sequencing reinforced the notion that genes are not the only players that determine a phenotype. Due to physiological or pathological fluctuations in gene expression, even genetically identical cells can behave and manifest different phenotypes under the same conditions. Here, we discuss mechanisms that can influence or even disrupt the axis between genotype and phenotype; the role of modifier genes, the general concept of genetic redundancy, genetic compensation, the recently described transcriptional adaptation, environmental stressors, and phenotypic plasticity. We furthermore highlight the usage of induced pluripotent stem cells (iPSCs), the generation of isogenic lines through genome engineering, and sequencing technologies can help extract new genetic and epigenetic mechanisms from what is hitherto considered 'noise'.

Bioprospecting and biotechnological insights into sweet-tasting proteins by microbial hosts-a review

Owing to various undesirable health effects of sugar overconsumption, joint efforts are being made by industrial sectors and regulatory authorities to reduce sugar consumption practices, worldwide. Artificial sweeteners are considered potential substitutes in several products, e.g., sugar alcohols (polyols), high-fructose corn syrup, powdered drink mixes, and other beverages. Nevertheless, their long-standing health effects continue to be debatable. Consequently, growing interest has been shifted in producing non-caloric sweetenersfrom renewable resources to meet consumers' dietary requirements. Except for the lysozyme protein, various sweet proteins including thaumatin, mabinlin, brazzein, monellin, miraculin, pentadin, and curculin have been identified in tropical plants. Given the high cost and challenging extortion of natural resources, producing these sweet proteins using engineered microbial hosts, such as Yarrowia lipolytica, Pichia pastoris, Hansenula polymorpha, Candida boidinii, Arxula adeninivorans, Pichia methanolica, Saccharomyces cerevisiae, and Kluyveromyces lactis represents an appealing choice. Engineering techniques can be applied for large-scale biosynthesis of proteins, which can be used in biopharmaceutical, food, diagnostic, and medicine industries. Nevertheless, extensive work needs to be undertaken to address technical challenges in microbial production of sweet-tasting proteins in bulk. This review spotlights historical aspects, physicochemical properties (taste, safety, stability, solubility, and cost), and recombinant biosynthesis of sweet proteins. Moreover, future opportunities for process improvement based on metabolic engineering strategies are also discussed.

Nematode chromosomes

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.

Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family

The fungal cell wall, comprised primarily of protein and polymeric carbohydrate, maintains cell structure, provides protection from the environment, and is an important antifungal drug target. Pir proteins (proteins with internal repeats) are linked to cell wall β-1,3-glucan and are best studied in Saccharomyces cerevisiae. Sequential deletion of S. cerevisiae PIR genes produces strains with increasingly notable cell wall damage. However, a true null mutant lacking all five S. cerevisiae PIR genes was never constructed. Because only two PIR genes (PIR1, PIR32) were annotated in the Candida albicans genome, the initial goal of this work was to construct a true Δpir/Δpir null strain in this species. Unexpectedly, the phenotype of the null strain was almost indistinguishable from its parent, leading to the search for other proteins with Pir function. Bioinformatic approaches revealed nine additional C. albicans proteins that share a conserved Pir functional motif (minimally DGQ). Examination of the protein sequences revealed another conserved motif (QFQFD) toward the C-terminal end of each protein. Sequence similarities and presence of the conserved motif(s) were used to identify a set of 75 proteins across 16 fungal species that are proposed here as Pir proteins. The Pir family is greatly expanded in C. albicans and C. dubliniensis compared to other species and the orthologs are known to have specialized function during chlamydospore formation. Predicted Pir structures showed a conserved core of antiparallel beta-sheets and sometimes-extensive loops that contain amino acids with the potential to form linkages to cell wall components. Pir phylogeny demonstrated emergence of specific ortholog groups among the fungal species. Variation in gene expression patterns was noted among the ortholog groups during growth in rich medium. PIR allelic variation was quite limited despite the presence of a repeated sequence in many loci. Results presented here demonstrate that the Pir family is larger than previously recognized and lead to new hypotheses to test to better understand Pir proteins and their role in the fungal cell wall.

Mitochondrial ribosomal protein genes connected with Alzheimer's and tellurite toxicity

Mitochondrial diseases are a group of genetic disorders characterized by dysfunctional mitochondria. Within eukaryotic cells, mitochondria contain their own ribosomes, which synthesize small amounts of proteins, all of which are essential for the biogenesis of the oxidative phosphorylation system. The ribosome is an evolutionarily conserved macromolecular machine in nature both from a structural and functional point of view, universally responsible for the synthesis of proteins. Among the diseases afflicting humans, those of ribosomal origin - either cytoplasmic ribosomes (80S) or mitochondrial ribosomes (70S) - are relevant. These are inherited or acquired diseases most commonly caused by either ribosomal protein haploinsufficiency or defects in ribosome biogenesis. Here we review the scientific literature about the recent advances on changes in mitochondrial ribosomal structural and assembly proteins that are implicated in primary mitochondrial diseases and neurodegenerative disorders, and their possible connection with metalloid pollution and toxicity, with a focus on MRPL44, NAM9 (MNA6) and GEP3 (MTG3), whose lack or defect was associated with resistance to tellurite. Finally, we illustrate the suitability of yeast Saccharomyces cerevisiae (S.cerevisiae) and the nematode Caenorhabditis elegans (C.elegans) as model organisms for studying mitochondrial ribosome dysfunctions including those involved in human diseases.

Visualising the next frontiers in wine yeast research

A range of game-changing biodigital and biodesign technologies are coming of age all around us, transforming our world in complex ways that are hard to predict. Not a day goes by without news of how data-centric engineering, algorithm-driven modelling, and biocyber technologies—including the convergence of artificial intelligence, machine learning, automated robotics, quantum computing, and genome editing—will change our world. If we are to be better at expecting the unexpected in the world of wine, we need to gain deeper insights into the potential and limitations of these technological developments and advances along with their promise and perils. This article anticipates how these fast-expanding bioinformational and biodesign toolkits might lead to the creation of synthetic organisms and model systems, and ultimately new understandings of biological complexities could be achieved. A total of four future frontiers in wine yeast research are discussed in this article: the construction of fully synthetic yeast genomes, including minimal genomes; supernumerary pan-genome neochromosomes; synthetic metagenomes; and synthetic yeast communities. These four concepts are at varying stages of development with plenty of technological pitfalls to overcome before such model chromosomes, genomes, strains, and yeast communities could illuminate some of the ill-understood aspects of yeast resilience, fermentation performance, flavour biosynthesis, and ecological interactions in vineyard and winery settings. From a winemaker's perspective, some of these ideas might be considered as far-fetched and, as such, tempting to ignore. However, synthetic biologists know that by exploring these futuristic concepts in the laboratory could well forge new research frontiers to deepen our understanding of the complexities of consistently producing fine wines with different fermentation processes from distinctive viticultural terroirs. As the saying goes in the disruptive technology industry, it take years to create an overnight success. The purpose of this article is neither to glorify any of these concepts as a panacea to all ills nor to crucify them as a danger to winemaking traditions. Rather, this article suggests that these proposed research endeavours deserve due consideration because they are likely to cast new light on the genetic blind spots of wine yeasts, and how they interact as communities in vineyards and wineries. Future-focussed research is, of course, designed to be subject to revision as new data and technologies become available. Successful dislodging of old paradigms with transformative innovations will require open-mindedness and pragmatism, not dogmatism—and this can make for a catch-22 situation in an archetypal traditional industry, such as the wine industry, with its rich territorial and socio-cultural connotations.

Fungi in Freshwaters: Prioritising Aquatic Hyphomycetes in Conservation Goals

Deprivation of protection for aquatic hyphomycetes is disturbing because they are key players in freshwater ecosystems across the globe. To attain a more holistic conservation paradigm for biodiversity in freshwaters, it is necessary to broaden our ecological perception of microfungi, mainly in aquatic hyphomycetes. A considerable groundwork still needs to be accomplished in progressing towards conserving aquatic hyphomycetes. Overcoming the paucity of information regarding the rare and endangered species, biogeography and above all, a global biodiversity database, would be a significant contribution in the initiation of an overarching conservation strategy for aquatic hyphomycetes. Being aware that the biodiversity decline in freshwaters is alarming, here we seek to explore why biodiversity data of aquatic hyphomycetes are missing. This article closely examines the threats to the biodiversity of aquatic hyphomycetes and freshwater ecosystems. Moving forward, we advocate a structured approach to gaining a thorough understanding to embrace aquatic hyphomycetes biodiversity into the conservation strategies. Including aquatic hyphomycetes in the conservation objectives may attract more funding opportunities for global surveys to initiate a fungal inclusive conservation era. Fungal conservation ventures can profit from interdisciplinary collaborations and cutting-edge science and technology, leading to informed decision making for biodiversity assessment and management.

Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi, the First Novel Eukaryote Isolated from the International Space Station

Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and 5% CO₂ conditions. Confocal, scanning, and transmission electron microscopy revealed distinct morphological differences between the microgravity-grown cells and the standard Earth gravity-grown cells, including larger cells and thicker cell walls, altered intracellular morphology, modifications to extracellular fimbriae, budding, and the shedding of bud scars. Phylogenetic analyses via multi-locus sequence typing indicated that these ISS strains represented a single species in the genus Naganishia and were clustered with Naganishia diffluens. The name Naganishia tulchinskyi is proposed to accommodate these strains, with IF6SW-B1^T as the holotype. The gene ontologies were assigned to the cell morphogenesis, microtubule-based response, and response to UV light, suggesting a variety of phenotypes that are well suited to respond to microgravity and radiation. Genomic analyses also indicated that the extracellular region, outer membrane, and cell wall were among the highest cellular component results, thus implying a set of genes associated with Titan-like cell plasticity. Finally, the highest molecular function matches included cytoskeletal motor activity, microtubule motor activity, and nuclear export signal receptor activity.

Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies

Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.

Evolutionary engineering to improve Wickerhamomyces subpelliculosus and Kazachstania gamospora for baking

The conventional baker's yeast, Saccharomyces cerevisiae, is the indispensable baking yeast of all times. Its monopoly coupled to its major drawbacks, such as streamlined carbon substrate utilisation base and a poor ability to withstand a number of baking associated stresses, prompt the need to search for alternative yeasts to leaven bread in the era of increasingly complex consumer lifestyles. Our previous work identified the inefficient baking attributes of Wickerhamomyces subpelliculosus and Kazachstania gamospora as well as preliminarily observations of improving the fermentative capacity of these potential alternative baker's yeasts using evolutionary engineering. Here we report on the characterisation and improvement in baking traits in five out of six independently evolved lines incubated for longer time and passaged for at least 60 passages relative to their parental strains as well as the conventional baker's yeast. In addition, the evolved clones produced bread with a higher loaf volume when compared to bread baked with either the ancestral strain or the control conventional baker's yeast. Remarkably, our approach improved the yeasts' ability to withstand baking associated stresses, a key baking trait exhibited poorly in both the conventional baker's yeast and their ancestral strains. W. subpelliculosus evolved the best characteristics attractive for alternative baker's yeasts as compared to the evolved K. gamospora strains. These results demonstrate the robustness of evolutionary engineering in development of alternative baker's yeasts.

The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae

The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.

Small Proteins in Archaea, a Mainly Unexplored World

In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.

Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases

Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.

Principles and correction of 5'-splice site selection

In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.

The dark side of the ribosome life cycle

Thanks to genetics, biochemistry, and structural biology many features of the ribosome´s life cycles in models of bacteria, eukaryotes, and some organelles have been revealed to near-atomic details. Collectively, these studies have provided a very detailed understanding of what are now well-established prototypes for ribosome biogenesis and function as viewed from a 'classical' model organisms perspective. However, very important challenges remain ahead to explore the functional and structural diversity of both ribosome biogenesis and function across the biological diversity on earth. Particularly, the 'third domain of life', the archaea, and also many non-model bacterial and eukaryotic organisms have been comparatively neglected. Importantly, characterizing these additional biological systems will not only offer a yet untapped window to enlighten the evolution of ribosome biogenesis and function but will also help to unravel fundamental principles of molecular adaptation of these central cellular processes.

Saccharomyces cerevisiae as a Heterologous Host for Natural Products

Cell factories can provide a sustainable supply of natural products with applications as pharmaceuticals, food-additives or biofuels. Besides being an important model organism for eukaryotic systems, Saccharomyces cerevisiae is used as a chassis for the heterologous production of natural products. Its success as a cell factory can be attributed to the vast knowledge accumulated over decades of research, its overall ease of engineering and its robustness. Many methods and toolkits have been developed by the yeast metabolic engineering community with the aim of simplifying and accelerating the engineering process.In this chapter, a range of methodologies are highlighted, which can be used to develop novel natural product cell factories or to improve titer, rate and yields of an existing cell factory with the goal of developing an industrially relevant strain. The addressed topics are applicable for different stages of a cell factory engineering project and include the choice of a natural product platform strain, expression cassette design for heterologous or native genes, basic and advanced genetic engineering strategies, and library screening methods using biosensors. The many engineering methods available and the examples of yeast cell factories underline the importance and future potential of this host for industrial production of natural products.

Quantitative Proteomics in Yeast : From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores

Simple light isotope metabolic labeling (bSLIM) is an innovative method to accurately quantify differences in protein abundance at the proteome level in standard bottom-up experiments. The quantification process requires computation of the ratio of intensity of several isotopologs in the isotopic cluster of every identified peptide. Thus, appropriate bioinformatic workflows are required to extract the signals from the instrument files and calculate the required ratio to infer peptide/protein abundance. In a previous study (Sénécaut et al., J Proteome Res 20:1476-1487, 2021), we developed original open-source workflows based on OpenMS nodes implemented in a KNIME working environment. Here, we extend the use of the bSLIM labeling strategy in quantitative proteomics by presenting an alternative procedure to extract isotopolog intensities and process them by taking advantage of new functionalities integrated into the Minora node of Proteome Discoverer 2.4 software. We also present a graphical strategy to evaluate the statistical robustness of protein quantification scores and calculate the associated false discovery rates (FDR). We validated these approaches in a case study in which we compared the differences between the proteomes of two closely related yeast strains.

Intrinsic Strand-Incision Activity of Human UNG: Implications for Nick Generation in Immunoglobulin Gene Diversification

Uracil arises in cellular DNA by cytosine (C) deamination and erroneous replicative incorporation of deoxyuridine monophosphate opposite adenine. The former generates C → thymine transition mutations if uracil is not removed by uracil-DNA glycosylase (UDG) and replaced by C by the base excision repair (BER) pathway. The primary human UDG is hUNG. During immunoglobulin gene diversification in activated B cells, targeted cytosine deamination by activation-induced cytidine deaminase followed by uracil excision by hUNG is important for class switch recombination (CSR) and somatic hypermutation by providing the substrate for DNA double-strand breaks and mutagenesis, respectively. However, considerable uncertainty remains regarding the mechanisms leading to DNA incision following uracil excision: based on the general BER scheme, apurinic/apyrimidinic (AP) endonuclease (APE1 and/or APE2) is believed to generate the strand break by incising the AP site generated by hUNG. We report here that hUNG may incise the DNA backbone subsequent to uracil excision resulting in a 3´-α,β-unsaturated aldehyde designated uracil-DNA incision product (UIP), and a 5´-phosphate. The formation of UIP accords with an elimination (E2) reaction where deprotonation of C2´ occurs via the formation of a C1´ enolate intermediate. UIP is removed from the 3´-end by hAPE1. This shows that the first two steps in uracil BER can be performed by hUNG, which might explain the significant residual CSR activity in cells deficient in APE1 and APE2.

Mitophagy in Yeast: Decades of Research

Mitophagy, the selective degradation of mitochondria by autophagy, is one of the most important mechanisms of mitochondrial quality control, and its proper functioning is essential for cellular homeostasis. In this review, we describe the most important milestones achieved during almost 2 decades of research on yeasts, which shed light on the molecular mechanisms, regulation, and role of the Atg32 receptor in this process. We analyze the role of ROS in mitophagy and discuss the physiological roles of mitophagy in unicellular organisms, such as yeast; these roles are very different from those in mammals. Additionally, we discuss some of the different tools available for studying mitophagy.

Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content

The black yeast Exophiala lecanii-corni of the order Chaetothyriales is notable for its ability to produce abundant quantities of DHN-melanin. While many other Exophiala species are frequent causal agents of human infection, E. lecanii-corni CBS 102400 lacks the thermotolerance requirements that enable pathogenicity, making it appealing for use in targeted functional studies and biotechnological applications. Here, we report the stress tolerance characteristics of E. lecanii-corni, with an emphasis on the influence of melanin on its resistance to various forms of stress. We find that E. lecanii-corni has a distinct stress tolerance profile that includes variation in resistance to temperature, osmotic, and oxidative stress relative to the extremophilic and pathogenic black yeast Exophiala dermatitidis. Notably, the presence of melanin substantially impacts stress resistance in E. lecanii-corni, while this was not found to be the case in E. dermatitidis. The cellular context, therefore, influences the role of melanin in stress protection. In addition, we present a detailed analysis of the E. lecanii-corni genome, revealing key differences in functional genetic content relative to other ascomycetous species, including a significant decrease in abundance of genes encoding ribosomal proteins. In all, this study provides insight into how genetics and physiology may underlie stress tolerance and enhances understanding of the genetic diversity of black yeasts.

Using Genomics to Shape the Definition of the Agglutinin-Like Sequence (ALS) Family in the Saccharomycetales

The Candida albicans agglutinin-like sequence (ALS) family is studied because of its contribution to cell adhesion, fungal colonization, and polymicrobial biofilm formation. The goal of this work was to derive an accurate census and sequence for ALS genes in pathogenic yeasts and other closely related species, while probing the boundaries of the ALS family within the Order Saccharomycetales. Bioinformatic methods were combined with laboratory experimentation to characterize 47 novel ALS loci from 8 fungal species. AlphaFold predictions suggested the presence of a conserved N-terminal adhesive domain (NT-Als) structure in all Als proteins reported to date, as well as in S. cerevisiae alpha-agglutinin (Sag1). Lodderomyces elongisporus, Meyerozyma guilliermondii, and Scheffersomyces stipitis were notable because each species had genes with C. albicans ALS features, as well as at least one that encoded a Sag1-like protein. Detection of recombination events between the ALS family and gene families encoding other cell-surface proteins such as Iff/Hyr and Flo suggest widespread domain swapping with the potential to create cell-surface diversity among yeast species. Results from the analysis also revealed subtelomeric ALS genes, ALS pseudogenes, and the potential for yeast species to secrete their own soluble adhesion inhibitors. Information presented here supports the inclusion of SAG1 in the ALS family and yields many experimental hypotheses to pursue to further reveal the nature of the ALS family.

Isolation, identification, and characterization of wild budding yeasts from rose flowers in Fukuyama city, Hiroshima, Japan, and their application in bread and wine production

In this study, we isolated 741 wild budding yeast strains from the flowers of 45 rose cultivars growing in Fukuyama city, Hiroshima, Japan. Of these 741 strains, 21 were found to have high fermentation abilities in yeast extract-peptone-dextrose (YPD) medium. Four of the 21 strains were able to ferment bread dough to make bread. These yeasts were identified as Saccharomyces cerevisiae, Lachancea fermentati, Lachancea kluyveri, and a Torulaspora sp. based on DNA sequences from the 26S rDNA D1/D2 regions. The CO₂ production profiles of the bread dough generated by the rose yeasts were evaluated using a Fermograph. Saccharomyces cerevisiae FRY2915 exhibited the highest fermentation capacity. Furthermore, FRY2915 was able to ferment grape juice to produce wine, yielding an alcohol concentration of more than 12%. The four rose yeasts isolated during this study have the potential to produce various types of unique fermented foods, thus enhancing the value of the microbiota associated with rose flowers.

Studying Lipid-Related Pathophysiology Using the Yeast Model

Saccharomyces cerevisiae, commonly known as baker's yeast, is one of the most comprehensively studied model organisms in science. Yeast has been used to study a wide variety of human diseases, and the yeast model system has proved to be an especially amenable tool for the study of lipids and lipid-related pathophysiologies, a topic that has gained considerable attention in recent years. This review focuses on how yeast has contributed to our understanding of the mitochondrial phospholipid cardiolipin (CL) and its role in Barth syndrome (BTHS), a genetic disorder characterized by partial or complete loss of function of the CL remodeling enzyme tafazzin. Defective tafazzin causes perturbation of CL metabolism, resulting in many downstream cellular consequences and clinical pathologies that are discussed herein. The influence of yeast research in the lipid-related pathophysiologies of Alzheimer's and Parkinson's diseases is also summarized.

Point mutations in the squalene epoxidase erg1 and sterol 14-α demethylase erg11 gene of T indotineae isolates indicate that the resistant mutant strains evolved independently

BACKGROUND

The T indotineae population shows a high amount of terbinafine resistant isolates based on different point mutations of squalene epoxidase erg1 (ergosterol) gene. A significant proportion of these isolates also show azole resistance.

OBJECTIVES

Elucidation of the molecular mechanism for azole resistance, especially the identification of mutations in the sterol 14-α demethylase Erg11 genes, which encode for enzymes interacting with azoles.

METHODS

Sequencing of putative Erg11 genes and analysis of phenotypic resistance pattern using a microplate-laser-nephelometry-based growth assay.

RESULTS

Four different types of Erg11B mutants were detected; two double mutants with Ala230Thr/Asp441Gly, respectively, Ala230/Tyr444His and single mutants with Gly443Glu, Tyr444Cys and Tyr444His. All isolates featured the wild type genotype of Erg11A. All strains demonstrated different combinations of Erg1 and Erg11 genotypes.

CONCLUSION

Resistance against terbinafine and azoles developed several times independently within the T indotineae population. The challenge for fungal treatment is, therefore, that species identification is not enough for prediction of therapeutic efficacy of antifungals. In the future, it will also become important to analyse genes involved in resistance mechanisms.

A standard knockout procedure alters expression of adjacent loci at the translational level

The Saccharomyces cerevisiae gene deletion collection is widely used for functional gene annotation and genetic interaction analyses. However, the standard G418-resistance cassette used to produce knockout mutants delivers strong regulatory elements into the target genetic loci. To date, its side effects on the expression of neighboring genes have never been systematically assessed. Here, using ribosome profiling data, RT-qPCR, and reporter expression, we investigated perturbations induced by the KanMX module. Our analysis revealed significant alterations in the transcription efficiency of neighboring genes and, more importantly, severe impairment of their mRNA translation, leading to changes in protein abundance. In the ‘head-to-head’ orientation of the deleted and neighboring genes, knockout often led to a shift of the transcription start site of the latter, introducing new uAUG codon(s) into the expanded 5′ untranslated region (5′ UTR). In the ‘tail-to-tail’ arrangement, knockout led to activation of alternative polyadenylation signals in the neighboring gene, thus altering its 3′ UTR. These events may explain the so-called neighboring gene effect (NGE), i.e. false genetic interactions of the deleted genes. We estimate that in as much as ∼1/5 of knockout strains the expression of neighboring genes may be substantially (>2-fold) deregulated at the level of translation.

The metabolic growth limitations of petite cells lacking the mitochondrial genome

Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.

AI applications in functional genomics

We review the current applications of artificial intelligence (AI) in functional genomics. The recent explosion of AI follows the remarkable achievements made possible by "deep learning", along with a burst of "big data" that can meet its hunger. Biology is about to overthrow astronomy as the paradigmatic representative of big data producer. This has been made possible by huge advancements in the field of high throughput technologies, applied to determine how the individual components of a biological system work together to accomplish different processes. The disciplines contributing to this bulk of data are collectively known as functional genomics. They consist in studies of: i) the information contained in the DNA (genomics); ii) the modifications that DNA can reversibly undergo (epigenomics); iii) the RNA transcripts originated by a genome (transcriptomics); iv) the ensemble of chemical modifications decorating different types of RNA transcripts (epitranscriptomics); v) the products of protein-coding transcripts (proteomics); and vi) the small molecules produced from cell metabolism (metabolomics) present in an organism or system at a given time, in physiological or pathological conditions. After reviewing main applications of AI in functional genomics, we discuss important accompanying issues, including ethical, legal and economic issues and the importance of explainability.

Ty1 integrase is composed of an active N-terminal domain and a large disordered C-terminal module dispensable for its activity in vitro

Long-terminal repeat (LTR) retrotransposons are genetic elements that, like retroviruses, replicate by reverse transcription of an RNA intermediate into a complementary DNA (cDNA) that is next integrated into the host genome by their own integrase. The Ty1 LTR retrotransposon has proven to be a reliable working model to investigate retroelement integration site preference. However, the low yield of recombinant Ty1 integrase production reported so far has been a major obstacle for structural studies. Here we analyze the biophysical and biochemical properties of a stable and functional recombinant Ty1 integrase highly expressed in E.coli. The recombinant protein is monomeric and has an elongated shape harboring the three-domain structure common to all retroviral integrases at the N-terminal half, an extra folded region, and a large intrinsically disordered region at the C-terminal half. Recombinant Ty1 integrase efficiently catalyzes concerted integration in vitro, and the N-terminal domain displays similar activity. These studies that will facilitate structural analyses may allow elucidating the molecular mechanisms governing Ty1 specific integration into safe places in the genome.

Learning from Yeast about Mitochondrial Carriers

Mitochondria are organelles that play an important role in both energetic and synthetic metabolism of eukaryotic cells. The flow of metabolites between the cytosol and mitochondrial matrix is controlled by a set of highly selective carrier proteins localised in the inner mitochondrial membrane. As defects in the transport of these molecules may affect cell metabolism, mutations in genes encoding for mitochondrial carriers are involved in numerous human diseases. Yeast Saccharomyces cerevisiae is a traditional model organism with unprecedented impact on our understanding of many fundamental processes in eukaryotic cells. As such, the yeast is also exceptionally well suited for investigation of mitochondrial carriers. This article reviews the advantages of using yeast to study mitochondrial carriers with the focus on addressing the involvement of these carriers in human diseases.

FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution

Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs.

The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.

Are droplets really suitable for single-cell analysis? A case study on yeast in droplets

Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases. In this work, we assessed the effect of culturing cells in droplets on the cellular function using yeast morphology as an indicator. Quantitative morphological analysis using CalMorph, an image-analysis program, demonstrated that cells cultured in flasks, large droplets, and small droplets significantly differed morphologically. From these differences, we identified that the cell cycle was delayed in droplets during the G1 phase and during the process of bud growth likely due to the checkpoint mechanism and impaired mitochondrial function, respectively. Furthermore, comparing small and large droplets, cells cultured in large droplets were morphologically more similar to those cultured in a flask, highlighting the advantage of increasing the droplet size. These results highlight a potential source of bias in cell analysis using droplets and reinforce the significance of assessing culture conditions of microfluidic cultivation methods for specific study cases.

Metataxonomic Analysis of Grape Microbiota During Wine Fermentation Reveals the Distinction of Cyprus Regional terroirs

Wine production in Cyprus has strong cultural ties with the island's tradition, influencing local and foreign consumers' preferences and contributing significantly to Cyprus' economy. A key contributor to wine quality and sensorial characteristics development is the microbiota that colonizes grapes and performs alcoholic fermentation. Still, the microbial patterns of wines produced in different geographic regions (terroir) in Cyprus remain unknown. The present study investigated the microbial diversity of five terroirs in Cyprus, two from the PGI Lemesos region [Kyperounta (PDO Pitsilia) and Koilani (PDO Krasochoria)], and three from the PGI Pafos region [Kathikas (PDO Laona Akamas), Panayia, and Statos (PDO Panayia)], of two grape varieties, Xynisteri and Maratheftiko, using high-throughput amplicon sequencing. Through a longitudinal analysis, we examined the evolution of the bacterial and fungal diversity during spontaneous alcoholic fermentation. Both varieties were characterized by a progressive reduction in their fungal alpha diversity (Shannon index) throughout the process of fermentation. Additionally, the study revealed a distinct separation among different terroirs in total fungal community composition (beta-diversity) for the variety Xynisteri. Also, Kyperounta terroir had a distinct total fungal beta-diversity from the other terroirs for Maratheftiko. Similarly, a significant distinction was demonstrated in total bacterial diversity between the PGI Lemesos region and the PGI Pafos terroirs for grape juice of the variety Xynisteri. Pre-fermentation, the fungal diversity for Xynisteri and Maratheftiko was dominated by the genera Hanseniaspora, Aureobasidium, Erysiphe, Aspergillus, Stemphylium, Penicillium, Alternaria, Cladosporium, and Mycosphaerella. During and post-fermentation, the species Hanseniaspora nectarophila, Saccharomyces cerevisiae, Hanseniaspora guilliermondii, and Aureobasidium pullulans, became the predominant in most must samples. Regarding the bacterial diversity, Lactobacillus and Streptococcus were the predominant genera for both grape varieties in all stages of fermentation. During fermentation, an increase was observed in the relative abundance of some bacteria, such as Acetobacter, Gluconobacter, and Oenococcus oeni. Finally, the study revealed microbial biomarkers with statistically significant higher relative representation, associated with each geographic region and each grape variety, during the different stages of fermentation. The present study's findings provide an additional linkage between the grape microbial community and the wine terroir.

Genome sequencing guide: An introductory toolbox to whole-genome analysis methods

To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called "-omics," have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated, including anticipatory guides and discussion questions for active engagement in the classroom. Additionally, the Supporting Information includes a case study to apply technical and ethical concepts from the text.

Saccharomyces cerevisiae biomass as a source of next-generation food preservatives: Evaluating potential proteins as a source of antimicrobial peptides

Saccharomyces cerevisiae is the main biotechnological tool for the production of Baker's or Brewer's biomasses, largely applied in beverage and fermented-food production. Through its gene expression reprogramming and production of compounds that inactivate the growth of other microorganisms, S. cerevisiae is able to grow in adverse environments and in complex microbial consortia, as in fruit pulps and root flour fermentations. The distinct set of up-regulated genes throughout yeast biomass propagation includes those involved in sugar fermentation, ethanol metabolization, and in protective responses against abiotic stresses. These high abundant proteins are precursors of several peptides with promising health-beneficial activities such as antihypertensive, antioxidant, antimicrobial, immunomodulatory, anti-obesity, antidiabetes, and mitogenic properties. An in silico investigation of these S. cerevisiae derived peptides produced during yeast biomass propagation or induced by physicochemical treatments were performed using four algorithms to predict antimicrobial candidates encrypted in abundantly expressed stress-related proteins encoded by different genes like AHP1, TSA1, HSP26, SOD1, HSP10, and UTR2, or metabolic enzymes involved in carbon source utilization, like ENO1/2, TDH1/2/3, ADH1/2, FBA1, and PDC1. Glyceraldehyde-3-phosphate dehydrogenase and enolase II are noteworthy precursor proteins, since they exhibited the highest scores concerning the release of antimicrobial peptide candidates. Considering the set of genes upregulated during biomass propagation, we conclude that S. cerevisiae biomass, a food-grade product consumed and marketed worldwide, should be considered a safe and nonseasonal source for designing next-generation bioactive agents, especially protein encrypting antimicrobial peptides that display broad spectra activity and could reduce the emergence of microbial resistance while also avoiding cytotoxicity.

Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation

Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.

A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation

Yeasts constitute over 1,500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications, and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here, we propose a multiphase multiobjective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic model describing the time-varying culture environment. In addition, we proposed a multiphase multiobjective flux balance analysis to compute the dynamics of intracellular fluxes. We then compared the metabolism of S. cerevisiae and Saccharomyces uvarum strains in a rich medium fermentation. The model successfully explained the experimental data and brought novel insights into how cryotolerant strains achieve redox balance. The proposed model (along with the corresponding code) provides a comprehensive picture of the main steps occurring inside the cell during batch cultures and offers a systematic approach to prospect or metabolically engineering novel yeast cell factories.

IMPORTANCE Nonconventional yeast species hold the promise to provide novel metabolic routes to produce industrially relevant compounds and tolerate specific stressors, such as cold temperatures. This work validated the first multiphase multiobjective genome-scale dynamic model to describe carbon and nitrogen metabolism throughout batch fermentation. To test and illustrate its performance, we considered the comparative metabolism of three yeast strains of the Saccharomyces genus in rich medium fermentation. The study revealed that cryotolerant Saccharomyces species might use the γ-aminobutyric acid (GABA) shunt and the production of reducing equivalents as alternative routes to achieve redox balance, a novel biological insight worth being explored further. The proposed model (along with the provided code) can be applied to a wide range of batch processes started with different yeast species and media, offering a systematic and rational approach to prospect nonconventional yeast species metabolism and engineering novel cell factories.

Reprogramming of the Ethanol Stress Response in Saccharomyces cerevisiae by the Transcription Factor Znf1 and Its Effect on the Biosynthesis of Glycerol and Ethanol

High ethanol levels can severely inhibit the growth of yeast cells and fermentation productivity. The ethanologenic yeast Saccharomyces cerevisiae activates several well-defined cellular mechanisms of ethanol stress response (ESR); however, the involved regulatory control remains to be characterized. Here, we report a new transcription factor of ethanol stress adaptation called Znf1. It plays a central role in ESR by activating genes for glycerol and fatty acid production (GUP1, GPP1, GPP2, GPD1, GAT1, and OLE1) to preserve plasma membrane integrity. Importantly, Znf1 also activates genes implicated in cell wall biosynthesis (FKS1, SED1, and SMI1) and in the unfolded protein response (HSP30, HSP104, KAR1, and LHS1) to protect cells from proteotoxic stress. The znf1Δ strain displays increased sensitivity to ethanol, the endoplasmic reticulum (ER) stressor β-mercaptoethanol, and the cell wall-perturbing agent calcofluor white. To compensate for a defective cell wall, the strain lacking ZNF1 or its target SMI1 displays increased glycerol levels of 19.6% and 27.7%, respectively. Znf1 collectively regulates an intricate network of target genes essential for growth, protein refolding, and production of key metabolites. Overexpression of ZNF1 not only confers tolerance to high ethanol levels but also increases ethanol production by 4.6% (8.43 g/liter) or 2.8% (75.78 g/liter) when 2% or 20% (wt/vol) glucose, respectively, is used as a substrate, compared to that of the wild-type strain. The mutually stress-responsive transcription factors Msn2/4, Hsf1, and Yap1 are associated with some promoters of Znf1’s target genes to promote ethanol stress tolerance. In conclusion, this work implicates the novel regulator Znf1 in coordinating expression of ESR genes and illuminates the unifying transcriptional reprogramming during alcoholic fermentation.

IMPORTANCE The yeast S. cerevisiae is a major microbe that is widely used in food and nonfood industries. However, accumulation of ethanol has a negative effect on its growth and limits ethanol production. The Znf1 transcription factor has been implicated as a key regulator of glycolysis and gluconeogenesis in the utilization of different carbon sources, including glucose, the most abundant sugar on earth, and nonfermentable substrates. Here, the role of Znf1 in ethanol stress response is defined. Znf1 actively reprograms expression of genes linked to the unfolded protein response (UPR), heat shock response, glycerol and carbohydrate metabolism, and biosynthesis of cell membrane and cell wall components. A complex interplay among transcription factors of ESR indicates transcriptional fine-tuning as the main mechanism of stress adaptation, and Znf1 plays a major regulatory role in the coordination. Understanding the adaptive ethanol stress mechanism is crucial to engineering robust yeast strains for enhanced stress tolerance or increased ethanol production.

From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory

The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes.

Health-promoting properties of Saccharomyces cerevisiae var. boulardii as a probiotic; characteristics, isolation, and applications in dairy products

Saccharomyces cerevisiae var. boulardii (S. boulardii) has been isolated from lychee (Litchi chinensis), mangosteen fruit, kombucha, and dairy products like kefir. Dairy products containing S. boulardii have been revealed to possess potential probiotic activities owing to their ability to produce organic acids, essential enzymes, vitamins, and other important metabolites such as vanillic acid, phenyl ethyl alcohol, and erythromycin. S. boulardii has a wide spectrum of anti-carcinogenic, antibacterial antiviral, and antioxidant activity, and is known to reduce serum cholesterol levels. However, this yeast has mainly been prescribed for prophylaxis treatment of gastrointestinal infectious diseases, and stimulating the immune system in a number of commercially available products. The present comprehensive review article reviews the properties of S. boulardii related to their use in fermented dairy foods as a probiotic microorganism or starter culture. Technical aspects regarding the integration of this yeast into the dairy foods matrix its health advantages, therapeutic functions, microencapsulation, and viability in harsh conditions, and safety aspects are highlighted.