Biology subjects

Hartl, J.

Publications and source records attributed to Hartl, J..

6 recordsLinked to original sources

bioRxiv2026

Human metabolites modulate antifungal efficacy and reveal creatinine-mediated antagonism of flucytosine

Clearing fungal infections can fail, even when the causative pathogen is susceptible to antifungal drugs in vitro. The reasons for this discrepancy often remain unclear. Here, we report that human metabolites affect antifungal drug efficacy. Studying Saccharomyces cerevisiae, we observed that human serum and common growth supplements alter the minimal inhibitory concentrations (MIC) across major antifungal classes, including fluconazole (FLC) and flucytosine (5-FC). To identify causal metabolites, we generated a library reflecting the physiological concentrations of 67 abundant blood metabolites. Assessing their impact on fungal fitness in the presence of antifungals revealed that creatinine, owing to its structural similarity to 5-FC, reduced the uptake and efficacy of 5-FC in S. cerevisiae, Candida albicans, and Nakaseomyces glabratus. Notably, 5-FC efficacy in urinary tract infections can be limited, and creatinine is highly concentrated in urine. We show that creatinine levels in urine increase the MIC of 5-FC in N. glabratus by approximately 100-fold, while reducing creatinine concentration in urine enhances 5-FC efficacy. Together, our findings highlight that drug interactions with creatinine and other human metabolites can strongly influence the activity of antifungals.

biochemistry↗

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

A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects

Despite abundant genomic and phenotypic data across individuals and environments, the functional impact of most mutations on phenotype remains unclear. Here, we bridge this gap by linking genome to proteome in 800 meiotic progeny from an intercross between two closely related Saccharomyces cerevisiae isolates adapted to distinct niches. Modest genetic distance between the parents generated remarkable proteomic diversity that was amplified in the progeny and captured by 6,476 genotype-protein associations, over 1,600 of which we resolved to single variants. Proteomic adaptation emerged through the combined action of numerous cis- and trans-regulatory mutations, a regulatory architecture that was conserved across the species. Notably, trans-regulatory variants often arose in proteins not traditionally associated with gene regulation, such as enzymes. Moreover, the proteomic consequences of mutations predicted fitness under various stresses. Our study demonstrates that the collective action of natural genetic variants drives dramatic proteome diversification, with molecular consequences that forecast phenotypic outcomes. Highlights- Proteome diversity arises from natural genetic variants, with divergent proteomes in closely related parents and progeny. - Cis-regulatory elements had strong individual impacts, but coherent trans effects combined to dominate protein expression. - Directional selection and frequent transgression suggest much of the proteome is under selective pressure. - Many trans-regulators are enzymes or transporters, with fewer than 4% of pQTLs linking known interactors. - Genome-to-proteome connections predicted the fitness impact of mutations under various stresses, including a strong but hidden causal variant in IRA2/NF1.

systems biology↗

bioRxiv2024

The Molecular Landscape of Cellular Metal Ion Biology

Metal ions play crucial roles in cells, yet the broader impact of metal availability on biological networks remains underexplored. We generated genome-wide resources, systematically quantifying yeast cell growth, metallomic, proteomic, and genetic responses upon varying each of its essential metal ions (Ca, Cu, Fe, K, Mg, Mn, Mo, Na, Zn), over several orders of magnitude. We find that metal ions deeply impact cellular networks, with 57.6% of the proteome, including most signalling pathways, responding. While the biological response to each metal is distinct, our data reveals common properties of metal responsiveness, such as concentration interdependencies and metal homeostasis. We describe a compendium of metal-dependent cellular processes and reveal that several understudied genes can be functionally annotated based on their metal responses. Furthermore, we report that metalloenzymes occupy central nodes in the metabolic network and are more likely to be encoded by isozymes, resulting in system-wide responsiveness to metal availability.

systems biology↗

bioRxiv2022

High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA

The ability to conduct high-quality proteomic experiments in high throughput has opened new avenues in clinical research, drug discovery, and systems biology. Next to an increase in quantitative precision, recent developments in high-throughput proteomics have also gained proteomic depth, to the extent that earlier gaps between classic and high-throughput experiments have significantly narrowed. Here we introduce and benchmark Zeno SWATH, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) in order to increase proteomic depth and dynamic range in proteomic experiments. Combined with the high acquisition speed, these gains in sensitivity are particularly attractive for conducting high-throughput proteomics experiments with high chromatographic flow rates and fast gradients. We demonstrate that when combined with either micro-flow- or analytical-flow-rate chromatography, Zeno SWATH increases protein identification in complex samples 5- to 10-fold when compared to current SWATH acquisition methods on the same instrument. Using 20-min micro-flow chromatography, Zeno SWATH identified > 6,000 proteins from a 62.5 ng load of human cell lysate with more than 5,000 proteins consistently quantified in triplicate injections with a median CV of 6%. Using 5-min analytical-flow-rate chromatography (800 {micro}l/min), Zeno SWATH identified 4,907 proteins from a triplicate injection of 2 {micro}g of a human cell lysate; or more than 3,000 proteins from 250 ng tryptic digest. Zeno SWATH hence facilitates precise proteomic experiments with small sample amounts using a fast and robust high flow-rate chromatographic method, broadening the application space that requires precise proteomic experiments on a large scale.

biochemistry↗

bioRxiv2022

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which an organosulfur-auxotrophy caused by deletion of homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. We discovered that an uncharacterized gene YLL058Wp, herein named Hydrogen sulfide utilizing-1 (HSU1), acts as a homocysteine synthase and allows the cells to substitute for Met17p by re-assimilating hydrosulfide ions leaked from met17{Delta} cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity. SummarySulfur limitation activates a dormant hydrogen sulfide fixation route via a novel homocysteine synthase Hsu1p (YLL058Wp).

molecular biology↗