Biology subjects

Berman, J.

Publications and source records attributed to Berman, J..

At least 19 recordsLinked to original sources

bioRxiv2026

J-AST: a web-based analysis platform for antimicrobial susceptibility testing

Antimicrobial resistance and tolerance pose escalating global health threats, necessitating reproducible and accessible tools for antimicrobial susceptibility testing (AST). While disk diffusion assays (DDAs) and Epsilometer tests (Etests) are widely used, there are limited open-source tools to analyze them. We present J-AST, a free, open-source, web-based platform for analyzing both DDAs and Etests. It provides automated and interactive annotation of regions of interest and metadata management, and quantifies microbial resistance and tolerance. J-AST outputs correlate strongly with those of existing tools, and equivalent DDA and Etest results correlate strongly with each other. The automated MIC detection achieved >90% agreement with manual readouts. J-AST is deployable both as desktop software and cloud service, unifies automated analysis with interactive review, and advances both fundamental research and clinical AST workflows.

bioinformatics↗

bioRxiv2026

Short chain fatty acids potentiate azoles by reprogramming fungal acetyl-CoA metabolism

Pathogens colonise metabolically diverse host environments. How metabolites found in host environments regulate antimicrobial drug susceptibility remains to be fully understood. Here we report on the roles of gut metabolites, short chain fatty acids (SCFAs), in antifungal drug susceptibility of the gut commensal and fungal pathogen Candida albicans. A genetic screen revealed that C. albicans mutants in peroxisome biogenesis display increased tolerance to the antifungal drug fluconazole. Peroxisomes are important for the metabolism of SCFAs by {beta}-oxidation, and exposure to the SCFAs butyrate and crotonate increased susceptibility and reduced tolerance to fluconazole. To understand if SCFAs inhibit fluconazole tolerance through their ability to inhibit histone deacetylases (HDACs), we compared them with the HDAC inhibitor trichostatin A. These experiments did not reveal an obvious connection between the degree of HDAC inhibition and the degree of fluconazole tolerance reduction. Exposure of C. albicans to crotonate and butyrate revealed transcriptional reprogramming involving remodelling of acetyl-CoA metabolism by upregulation of genes for {beta}-oxidation, peroxisome biogenesis and intracellular transport of acetyl-CoA, while the expression of ergosterol biosynthesis genes was reduced. Since ergosterol gene expression is required to overcome fluconazole stress, these results explain how SCFAs reduce fluconazole tolerance. Taken together, our results implicate peroxisome biogenesis and metabolism in fluconazole susceptibility. We posit that balanced acetyl-CoA metabolism promotes sufficient ergosterol biosynthesis to overcome fluconazole stress and drive tolerant growth. These pathways are perturbed by metabolic changes induced by SCFAs. These findings add to our understanding of the importance of metabolic regulation in antimicrobial drug responses. SIGNIFICANCEMetabolites produced by microbiota or host cells regulate microbial metabolism, physiology and drug responses. In the gut, the human commensal and pathogen Candida albicans is exposed to short-chain fatty acids made by bacteria. C. albicans metabolises short-chain fatty acids via peroxisomal {beta}-oxidation. Additionally, short-chain fatty acids change gene expression by inhibiting histone deacetylases. We found that short-chain fatty acids increase the susceptibility of C. albicans to the antifungal drug fluconazole and reduce fluconazole tolerance. Our mechanistic studies indicate that metabolic utilisation of short-chain fatty acids by C. albicans reduces fluconazole tolerance by changing acetyl-CoA metabolism and causing lower expression of ergosterol biosynthesis genes. Thus, short-chain fatty acids increase fluconazole susceptibility by changing fungal metabolism, while inhibition of histone deacetylases may play a more minor role. These findings shed light on the roles of metabolism and abundant gut metabolites in tolerance to a front-line antifungal drug.

microbiology↗

bioRxiv2026

Quiescence improves Candida albicans survival of fungicidal drug exposure

Quiescence, defined as the reversible exit from mitotic division and proliferative growth, is the predominant state of all microbes. Despite its prevalence, the properties and consequences of quiescence in Candida albicans, an opportunistic fungal pathogen, remain largely unexplored. In this study, we characterized the morphological, molecular, and biophysical properties of quiescent C. albicans cells and assessed the effects of quiescence on antifungal drug efficacy. Quiescent cells that were induced via carbon starvation in rich and minimal media underwent distinct morphological changes upon entry into quiescence; this included an increase in cell buoyant density, altered fluidity of the cytoplasm and nucleus, and remodeling of mitochondria. Most C. albicans cells arrested in an unbudded G1/G0 state, although a significant fraction of cells had budded morphologies and 4N DNA content, indicating that they arrested at other cell cycle phases. Both budded and unbudded quiescent cells efficiently re-entered the cell cycle upon nutrient replenishment, with time-to-quiescence exit varying depending on the total nutritional quality of the medium. Quiescence was associated with large-scale gene expression remodeling, including downregulation of ribosomal biogenesis genes and upregulation of autophagy and stress response pathways. Notably, a greater proportion of quiescent cells than proliferative cells survived exposure to the commonly used antifungal drugs micafungin, caspofungin, and amphotericin B in genetically diverse strains. Thus, quiescence is a distinct cellular state with important implications for antifungal drug efficacy in C. albicans. Author SummaryWe show that Candida albicans, a common fungal pathogen, can enter a reversible, non-dividing state when starved of carbon. Starved cells become smaller and denser, reorganize their mitochondria, change how densely packed the inside of the cell and its nucleus are, and switch on stress-protection and internal recycling programs while reducing protein synthesis activity. Most cells have ceased to actively divide, but many retained budded shapes and could restart growth when nutrients returned; the timing of recovery depended on the nutritional environment in which quiescence was initiated. Critically, quiescent cells from laboratory and clinical strains exhibited greater survival than proliferative cells when exposed to widely used fungicidal drugs including micafungin, caspofungin, and amphotericin B. These findings indicate that quiescence is an active, adaptive physiological state that helps Candida albicans survive hostile environmental conditions such as temperature stress and drug exposure. Accounting for the metabolic state of fungal cells in diagnostics and drug development may improve treatment outcomes.

microbiology↗

bioRxiv2025

Tolerance to the antifungal drug fluconazole is mediated by tuning cytoplasmic fluidity

Treatment failure rates for fungal infections cannot be explained simply by increased rates of drug resistance. Antifungal drug tolerance, the ability of a susceptible isolate to grow in the presence of inhibitory drug concentrations, relies upon a broad set of stress response pathways and can contribute to antifungal drug treatment failures. As the physical properties of the cytoplasm are critical for diverse cellular processes, we investigated whether cytoplasmic mesoscale fluidity is linked to antifungal tolerance, taking advantage of a fluorescent microrheological probe. Here, we show either using fluconazole, a common drug that inhibits ergosterol biosynthesis, or mutants in the ergosterol biosynthesis pathway, that cytoplasmic fluidity decreased and could be reversed upon drug removal. Reducing ribosome concentration decreased drug tolerance and restored cytoplasmic fluidity, highlighting a link between tolerance and cytoplasmic crowding and/or viscosity. However, growth in fluconazole did not increase ribosome concentrations; rather growth in fluconazole increased the number of dormant, hibernating ribosomes, cytoplasmic protein concentration, viscosity and condensate formation. Specifically, growth in fluconazole resulted in a substantial increase in processing bodies (P-bodies), whose presence correlated with azole tolerance. Furthermore, we found a substantial increase in cell-cell heterogeneity in all biophysical, biochemical and molecular outputs analyzed. Together, our results reveal that changes in the physical properties of the cytoplasm occur in response to antifungal drug and suggest that these changes, as well as increased cell-cell heterogeneity, are crucial for survival in fungistatic drugs.

microbiology↗

bioRxiv2025

Sphingolipid Homeostasis, Mitochondrial Activity, and PKA Signaling Drive an Azole-Tolerant State

Antifungal therapies frequently fail, resulting in persistent infections caused by the important opportunistic pathogen, Candida albicans, which is highly tolerant to azole drugs. Tolerance arises from a subpopulation of cells that survive prolonged drug exposure, yet the underlying mechanisms remain poorly defined. Here, transcription factor mutant library screens identified Mnl1 as a key repressor of tolerance. Loss of MNL1 elevated cAMP levels and activated the PKA pathway, linking Mnl1 to growth control and stress responses. Additionally, mnl1 cells exhibited altered sphingolipid composition, implicating Mnl1 in regulating membrane permeability, a key determinant of drug efflux and membrane integrity. Increased tolerance in mnl1 cells was also linked to increased mitochondrial function. Thus, Mnl1 regulates tolerance through coordinated control of sphingolipid metabolism, mitochondrial activity, and PKA signaling, highlighting that tolerant cells adopt a distinct physiological state primed to withstand antifungal stress.

microbiology↗

bioRxiv2024

Stress-driven emergence of heritable non-genetic drug resistance

Drug resistance is the chief cause of treatment failure for therapies targeting chronic and infectious diseases. Whether the emergence of resistance is accelerated by environmental exposure to low levels of therapeutics remains controversial. Here, we report a non-genetic mechanism of stress adaptation that promotes heritable resistance to the widely used antifungal drug fluconazole. In the human fungal pathogen Candida albicans, transient exposure to subtherapeutic fluconazole doses induces a protective response that we term para-resistance. Like conventional resistance mechanisms, para-resistance is heritable. However, it does not arise from genetic mutations and can revert spontaneously. Systematic analyses of para-resistant isolates suggest that its key regulators include the stress-activated MAP kinase Hog1, the histone deacetylase subunit Snt1, the chromatin regulator Rap1, and the Sko1 transcriptional factor. Notably, molecules that disrupt biomolecular condensation and prion propagation - crucial for the inheritance of protein assemblies - block the induction of para-resistance, whereas inhibiting histone deacetylases facilitates its induction. We find that para-resistance is common in clinical isolates and, remarkably, passage through the mammalian gut triggers its acquisition, compromising fluconazoles therapeutic efficacy. Our work defines a pervasive, prion-like epigenetic mechanism of stress adaptation and highlights potential strategies to mitigate the rapid emergence of drug resistance.

microbiology↗

bioRxiv2024

Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance in Candida albicans

BackgroundFungal infections are an increasing concern, particularly among immunocompromised patients and those with comorbidities who require multiple medications. However, the effects of drugs targeting human pathways on fungal cells, and whether they influence antifungal drug responses, are poorly understood. MethodsWe systematically analyzed clinical guidelines to shortlist non-antifungal drugs commonly used in conditions that increase the likelihood of fungal infections. Focusing on the most prevalent fungal pathogen, we then tested how these drugs affected the antifungal response of Candida albicans to two commonly used antifungals, fluconazole and anidulafungin. Drug interactions identified were further assessed using checkerboard and disk diffusion assays. Finally, antifungal treatment efficacy of fluconazole in combination with negatively interacting drugs was evaluated in an in vivo Galleria mellonella model of disseminated C. albicans infection. FindingsOut of 119 drugs frequently co-administered with antifungals in 40 conditions associated with a high risk of fungal infections, 34 compounds affected the antifungal drug response in C. albicans, with most drugs reducing or antagonising antifungal efficacy, several through increasing resistance or tolerance. Notably, fluconazole combinations with carvedilol and loperamide promoted antifungal resistance in both fungal cultures and in Galleria mellonella. InterpretationOur findings suggest that medications frequently taken by patients at risk of fungal infections regularly act on the fungal pathogens and can affect the effectiveness of antifungals. We propose that human drugs acting on fungal pathogens may be an underestimated factor contributing to the evolution of antifungal tolerance and resistance.

microbiology↗

bioRxiv2024

The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution

The functions of cells and proteins depend on their biochemical microenvironment. To understand how biochemical constraints shaped protein structural evolution, we coupled the extensive genetic and metabolic data from the Saccharomycotina subphylum with the capability of AlphaFold2 to systematically predict protein structures from sequence. Determining how 11,269 enzyme structures catalysing 361 different metabolic reactions evolved over 400 million years alongside their molecular functions, we report that metabolism has shaped the structural evolution of enzymes at different levels: the organisms overall metabolism; the topological organisation of the metabolic network; and each enzymes molecular properties. For example, structural evolution depends on each enzymes reaction mechanism, on the variability rather than the amount of metabolic flux, and on biosynthetic cost. Evolutionary cost-optimization is stronger on highly abundant enzymes and acts differently on different structural domains, with the exception of small-molecule binding sites, which are prioritised over other structural domains and lack cost-optimisation. Finally, while enzyme surfaces are less constrained, surface residues can also be exposed to positive selection for the co-evolution of protein-protein interaction sites. Accessing AlphaFolds power to predict protein structures systematically and across species barriers, facilitating the integration of protein structures with functional genomics, we were thus able to map biological constraints which shape protein structural evolution at scale and over long timelines.

systems biology↗

bioRxiv2024

Step-wise evolution of azole resistance through copy number variation followed by KSR1 loss of heterozygosity in Candida albicans.

Antimicrobial drug resistance poses a global health threat, requiring a deeper understanding of the evolutionary processes that lead to its emergence in pathogens. Complex evolutionary dynamics involve multiple mutations that can result in cooperative or competitive (clonal interference) effects. Candida albicans, a major fungal pathogen, displays high rates of copy number variation (CNV) and loss of heterozygosity (LOH). CNV and LOH events involve large numbers of genes and could synergize during evolutionary adaptation. Understanding the contributions of CNV and LOH to antifungal drug adaptation is challenging, especially in the context of whole-population genome sequencing. Here, we document the sequential evolution of fluconazole tolerance and then resistance in a C. albicans isolate involving an initial CNV on chromosome 4, followed by an LOH on chromosome R that involves KSR1. Similar LOH events involving KSR1, which encodes a reductase involved in sphingolipid biosynthesis, were also detected in independently evolved fluconazole resistant isolates. We dissect the specific KSR1 codons that affect fluconazole resistance and tolerance. The combination of the chromosome 4 CNV and KSR1 LOH results in a >500-fold increase in azole resistance, illustrating a compelling example of rapid, yet step-wise, interplay between CNV and LOH in drug resistance evolution.

microbiology↗

bioRxiv2022

Antifungal tolerance and resistance emerge at distinct drug concentrations and rely upon different aneuploid chromosomes

Antifungal drug tolerance is a response distinct from resistance, in which cells grow slowly above the minimum inhibitory drug concentration (MIC). Here we found that the majority (69.2%) of 133 Candida albicans clinical isolates, including standard lab strain SC5314, exhibited temperature-enhanced tolerance at 37{degrees}C and 39{degrees}C, and were not tolerant at 30{degrees}C. Other isolates were either always tolerant (23.3%) or never tolerant (7.5%) at these three temperatures, suggesting that tolerance requires different physiological processes in different isolates. At supra-MIC fluconazole concentrations (8-128 g/ml), tolerant colonies emerged rapidly at a frequency of ~10-3. In liquid passages over a broader range of fluconazole concentrations (0.25-128 g/ml), tolerance emerged rapidly (within one passage) at supra-MIC concentrations. By contrast, resistance appeared at sub-MIC concentrations after 5 or more passages. Of 155 adaptors that evolved higher tolerance, all carried one of several recurrent aneuploid chromosomes, often including chromosome R, alone or in combination with other chromosomes. Furthermore, loss of these recurrent aneuploidies was associated with a loss of acquired tolerance, indicating that specific aneuploidies confer fluconazole tolerance. Thus, genetic background and physiology, and the degree of drug stress (above or below the MIC) influence the evolutionary trajectories and dynamics with which antifungal drug resistance or tolerance emerges. ImportanceAntifungal drug tolerance differs from drug resistance: tolerant cells grow slowly in drug, while resistant cells usually grow well, due to mutations in a few known genes. More than half of Candida albicans clinical isolates have higher tolerance at body temperature than they do at the lower temperatures used for most lab experiments. This implies that different isolates achieve drug tolerance via several cellular processes. When we evolved different strains at a range of high drug concentrations above inhibitory levels, tolerance emerged rapidly and at high frequency (one in 1000 cells) while resistance only appeared later at very low drug concentrations. An extra copy of all or part of chromosome R was associated with tolerance, while point mutations or different aneuploidies were seen with resistance. Thus, genetic background and physiology, temperature, and drug concentration all influence how drug tolerance or resistance evolves.

evolutionary biology↗

bioRxiv2022

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. However, the use of one or few molecular markers can lead to inaccurate inferences of species history and errors in classification. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense dataset of 711 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provide profile Hidden Markov Models for each, facilitating others to use these molecular markers. Examination of the resulting genome-scale phylogeny: (1) helped resolve ongoing taxonomic controversies and identified new ones; (2) revealed extensive strain misidentification, underscoring the importance of population-level sampling in species classification; and (3) identified novel lineages that may shed light on the early evolution of an important genus. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the tree of life.

evolutionary biology↗

bioRxiv2022

Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to anti-fungal compounds

Candida albicans is an opportunistic human pathogen which represents a significant threat to human health and is associated with substantial socio-economic burden. Current antifungal treatments fail at least in part because C. albicans can initiate a strong drug tolerance response, allowing cells to grow at concentrations above their minimal inhibitory concentration. Our goal is to better characterize this cytoprotective tolerance program at the molecular single cell level. We present here a nano-liter droplet-based fungal single cell transcriptomics platform capable of profiling thousands of individual C. albicans SC5314 cells in an efficient manner. Profiles of untreated cells partition into three transcriptional clusters with each highlighting a cell cycle checkpoint coupled with specific metabolic and stress responses, as perhaps expected. After just two days post-treatment with fluconazole, surviving cells bifurcate into two distinct subpopulations: the so-called response involving upregulation of protein translation, rRNA processing and mitochondrial cellular respiration, and the {beta} response involving processes and stress responses that assist damaged cells. By extending our time series to six days and profiling with other antifungals and bioactive compounds, we provide evidence that surviving cells transition from the to {beta} responses mediated by the Ribosome Assembly Stress Response (RASTR).

microbiology↗

bioRxiv2022

Regulation of heme utilization and homeostasis in Candida albicans

Heme (iron-protoporphyrin IX) is an essential but potentially toxic cellular cofactor. While most organisms are heme prototrophs, many microorganisms can utilize environmental heme as iron source. The pathogenic yeast Candida albicans can utilize host heme in the iron-poor host environment, using an extracellular cascade of soluble anchored hemophores, and plasma membrane ferric reductase-like proteins. To gain additional insight into the C. albicans heme uptake pathway, we performed an unbiased genetic selection for mutants resistant to the toxic heme analog Ga3+-protoporphyrin IX at neutral pH, and a secondary screen for inability to utilize heme as iron source. Among the mutants isolated were the genes of the pH-responsive RIM pathway, and a zinc finger transcription factor, HUF1. In the presence of hemin in the medium, HUF1 is induced, the Huf1 protein is stabilized and Huf1-GFP localizes to the nucleus. In the huf1 mutant, cytoplasmic heme levels are elevated, while influx of extracellular heme is lower. Gene expression analysis indicated that in the presence of extracellular hemin, Huf1 activates the heme oxygenase HMX1, which breaks down excess cytoplasmic heme, while at the same time it also activates all the known heme uptake genes. These results indicate that Huf1 is a heme-responsive transcription factor that plays a role both in cytoplasmic heme homeostasis and in utilization of extracellular heme. The induction of heme uptake genes by Huf1 under iron satiety indicates that preferential utilization of host heme can be a dietary strategy in a heme prototroph.

microbiology↗

bioRxiv2022

The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids

Aneuploidy, an imbalance in chromosome copy numbers, causes genetic disorders, and drives cancer progression, drug tolerance, and antimicrobial resistance. While aneuploidy can confer stress resistance, it is not well understood how cells overcome the fitness burden caused by aberrant chromosomal copy numbers. Studies using both systematically generated 1-5 and natural aneuploid yeasts 6-8 triggered an intense debate about the role of dosage compensation, concluding that aneuploidy is transmitted to the transcriptome and proteome without significant buffering at the chromosome-wide level, and is, at least in lab strains, associated with significant fitness costs. Conversely, systematic sequencing and phenotyping of large collections of natural isolates revealed that aneuploidy is frequent and has few - if any - fitness costs in nature 9. To address these discrepant findings at the proteomic level, we developed a platform that yields highly precise proteomic measurements across large numbers of genetically diverse samples, and applied it to natural isolates collected as part of the 1011 genomes project 9. For 613 of the isolates, we were able to match the proteomes to their corresponding transcriptomes and genomes, subsequently quantifying the effect of aneuploidy on gene expression by comparing 95 aneuploid with 518 euploid strains. We find, as in previous studies, that aneuploid gene dosage is not buffered chromosome-wide at the transcriptome level. Importantly, in the proteome, we detect an attenuation of aneuploidy by about 25% below the aneuploid gene dosage in natural yeast isolates. Furthermore, this chromosome-wide dosage compensation is associated with the ubiquitin-proteasome system (UPS), which is expressed at higher levels and has increased activity across natural aneuploid strains. Thus, through systematic exploration of the species-wide diversity of the yeast proteome, we shed light on a long-standing debate about the biology of aneuploids, revealing that aneuploidy tolerance is mediated through chromosome-wide dosage compensation at the proteome level.

systems biology↗

bioRxiv2021

CRISPR Knock-in Designer: automatic oligonucleotide design software to introduce point mutations using CRISPR/Cas9

Knock-in of precise point mutations into protein-coding genes has been one of the earliest and most important applications of Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9. The ability to perform such precise gene editing is crucial to interrogate the function of specific protein residues and to create models of human diseases caused by protein amino acid changes. The homologous protein residues can be mutated in model animal species, and the consequences of these mutations can be studied, leading to a better understanding of the disease in question. Design of point mutation knock-in strategies has been a combination of manual steps assisted by several computational tools resulting in a time-consuming process and preventing a single rapid and integrated solution. We have therefore designed CRISPR Knock-in Designer, which can perform rapid and automatic design of point mutation knock-in DNA oligonucleotides upon provision of the mutation, a guide RNA, and essential identifier or sequence information. The tool supports most experimentally established CRISPR types and has multiple options for the resulting oligonucleotides to satisfy the needs of most users. We also provide allele-specific PCR-based and restriction enzyme-based genotyping strategies as part of the program output. CRISPR Knock-in Designer adjusts to the genomic context of any target codon and tries to design knock-in strategies when a codon straddles two exons, a situation we explored in whole genomes of several model species. CRISPR Knock-in Designer output can also be adapted for use with some of the newer Prime Editing design tools to facilitate the introduction of a specific mutation sequence using this advanced technology.

genetics↗

bioRxiv2021

The fitness costs and benefits of trisomy of each Candida albicanschromosome

Candida albicans is a prevalent human fungal pathogen. Rapid genomic change, due to aneuploidy, is a common mechanism that facilitates survival from multiple types of stresses including the few classes of available antifungal drugs. The stress survival of aneuploids occurs despite the fitness costs attributed to most aneuploids growing under idealized lab conditions. Systematic study of the aneuploid state in C. albicans has been hindered by the lack of a comprehensive collection of aneuploid strains. Here, we describe a collection of diploid C. albicans aneuploid strains, each carrying one extra copy of each chromosome, all from the same genetic background. We tested the fitness of this collection under several physiological conditions including shifts in pH, low glucose, oxidative stress, temperature, high osmolarity, membrane stress and cell wall stress. We found that, most aneuploids, under most conditions, were less fit than their euploid parent, yet there were specific conditions under which specific aneuploid isolates provided a fitness benefit relative to the euploid parent strain. Importantly, this fitness benefit was attributable to the change in the copy number of specific chromosomes. Thus, C. albicans can tolerate aneuploidy of each chromosome and some aneuploids confer improved growth under conditions that the yeast encounters in its host niches.

genetics↗

bioRxiv2020

Identification of essential genes and fluconazole resistance genes in Candida glabrata by profiling of Hermes transposon insertions.

Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from the CTG clade that includes Candida albicans. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and obtained more than 500,000 different semi-random insertions throughout the genome. Using machine learning, we identify up to 1278 protein-encoding genes (25% of total) that cannot tolerate transposon insertions and are thus essential for C. glabrata fitness in vitro. Interestingly, genes involved in mRNA splicing were less likely to be essential in C. glabrata than their orthologs in S. cerevisiae, whereas the opposite is true for genes involved in kinetochore function and chromosome segregation. Insertions in several known genes (e.g. PDR1, CDR1, PDR16, PDR17, UPC2A, DAP1) caused hypersensitivity to the first-line antifungal fluconazole, and we identify 12 additional genes that also contribute to innate fluconazole resistance (KGD1, KGD2, YHR045W, etc). Insertions in 200 other genes conferred significant resistance to fluconazole, two-thirds of which function in mitochondria and likely down-regulate Pdr1 expression or function. These findings show the utility of transposon insertion profiling in genome-wide forward-genetic investigations of fungal pathogens. IMPORTANCEPathogenic yeasts cause mucosal and systemic infections in millions of people each year. The innate resistance of Candida glabrata to fluconazole and its ability to acquire resistance to 2 other antifungals are contributing to its rise in incidence. Our understanding of C. glabrata biology has been hampered by inefficient genetic and genomic tools. This study addresses those deficiencies by developing powerful transposon mutagenesis strategies for the first time in this pathogen. We identify nearly all essential genes of C. glabrata that could be targeted for development of new antifungals. We generate large pools of random insertion mutants that can be easily monitored en masse with deep sequencing, thus enabling identification of genes involved in any number of biological processes. We identify dozens of new genes that increase or decrease innate resistance of clinical isolate BG2 to fluconazole and provide resources for further exploration of C. glabrata genetics and genomics.

genetics↗

bioRxiv2019

Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality

ABSTRACTIn vivo transposon mutagenesis, coupled with deep sequencing, enables large-scale genome-wide mutant screens for genes essential in different growth conditions. We analyzed six large-scale studies performed on haploid strains of three yeast species (Saccharomyces cerevisiae, Schizosaccaromyces pombe, and Candida albicans), each mutagenized with two of three different heterologous transposons (AcDs, Hermes, and PiggyBac). Using a machine-learning approach, we evaluated the ability of the data to predict gene essentiality. Important data features included sufficient numbers and distribution of independent insertion events. All transposons showed some bias in insertion site preference because of jackpot events, and preferences for specific insertion sequences and short-distance vs long-distance insertions. For PiggyBac, a stringent target sequence limited the ability to predict essentiality in genes with few or no target sequences. The machine learning approach also robustly predicted gene function in less well-studied species by leveraging cross-species orthologs. Finally, comparisons of isogenic diploid versus haploid S. cerevisiae isolates identified several genes that are haplo-insufficient, while most essential genes, as expected, were recessive. We provide recommendations for the choice of transposons and the inference of gene essentiality in genome-wide studies of eukaryotic haploid microbes such as yeasts, including species that have been less amenable to classical genetic studies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗