Biology subjects

Gacser, A.

Publications and source records attributed to Gacser, A..

10 recordsLinked to original sources

bioRxiv2026

A preclinical resistance framework discovers the virulence risks of antibiotics in development

Several new antibiotics target multidrug-resistant pathogens, yet resistance is still evaluated mainly by drug-susceptibility, leaving consequences for bacterial pathogenicity poorly understood. Here, we develop a framework integrating resistance evolution, genomic surveillance and host-pathogen phenotyping to classify antibiotics by resistance potential and pathogenic consequences. Applying this framework to Klebsiella pneumoniae identified functionally distinct antibiotic candidates associated with elevated virulence risk. Resistance evolution rapidly increased virulence through clinically-relevant mutations, without direct selection for pathogenicity. Despite distinct genetic routes, resistance converged on cell-envelope rewiring. A single resistance mutation increased epithelial adhesion, intracellular colonization, macrophage immune-evasion, and tissue persistence in murine infection models, transforming K. pneumoniae into a more invasive and cytotoxic pathogen. Risk-profile analysis revealed partial decoupling of resistance and pathogenicity, with some low-resistance antibiotics yielding highly-virulent populations. These findings establish resistance-driven virulence as an underappreciated translational hazard and call for incorporating host-pathogen interactions into resistance surveillance and preclinical antibiotic development.

microbiology↗

bioRxiv2025

Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization

In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of commensal bacteria to identify bacteria-derived inhibitors of fungal growth, with valeric and butyric acid as top hits. Experimental validation confirmed in silico predictions in three systems. First, in patient fecal samples, valeric and butyric acid levels inversely correlated with C. parapsilosis growth. Second, in vitro, valeric acid potently inhibited C. parapsilosis growth by causing intracellular acidification. Third, administration of glycerol valerate, and free or microencapsulated valeric acid blunted C. parapsilosis growth at murine intestinal sites where valeric acid could be detected. Thus, machine learning could identify a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of developing candidiasis during high-risk periods.

microbiology↗

bioRxiv2025

Early Candida - Oral Tumor Interactions Suggest miRNA-Mediated Regulation of Inflammatory and Tumor-associated processes

When simultaneously present, oral cancer and oral candidiasis are associated with high mortality. Recently, fungi-driven OSCC has emerged as a recognized phenomenon, that is triggered by Candida and sustained by several pro-tumor mechanisms. This study aimed to deepen our understanding and investigate how these mechanisms are regulated at the early stages of fungi-tumor interactions. Post-transcriptional regulation was examined through the analysis of miRNA (miR) responses in a metastatic cell line. We characterized early tumor responses to two common oral yeasts, C. albicans, frequently responsible for oral infections, and C. parapsilosis, a yeast with mostly commensal behavior in this niche. Exposed to C. albicans, tumor cells exhibited overexpression of inflammatory and pro-tumor pathways. This was also mirrored at the miR-level. Intriguingly, this species induced upregulation of oncogenic miRs, while simultaneously downregulated tumor-suppressive miRs. miR-target analyses revealed targets primarily to be involved in inflammation (TNFa signaling via NFKB), albeit tumor progression was also heavily influenced based on the targets identified within the PanCancer Progression Panel. Several miR-target pairs were identified with TRIB1-miR-30c-1-3p highlighted at the route of inflammation, and MMP3-miR-374a-3p and JUN-miR-1268b/miR-16-1-3p/miR-30c-1-3p at the route of OSCC progression. These findings highlight that C. albicans drives OSCC progression, in part, through miR regulation. Contrarily, C. parapsilosis elicited tumor responses predominantly related to hypoxia and metabolic regulation, followed by a mild activation of inflammatory and tumorigenic processes. No significant miR-regulatory responses were identified. To sum up, we added a new layer to fungi-tumor interactions and identified regulatory elements, that might hold future translational potential. ImportancePrevious studies have shown that yeast carriage in the oral cavity of oral cancer patients is significantly higher than those of healthy individuals. Additionally, the abundance of fungal cells is higher at malignant epithelial surfaces compared to the unaffected mucosal tissues. These observations indicated a direct interaction between mouth residing yeasts and oral tumorous cells. We have previously demonstrated that certain Candida species actively contribute to tumor progression in metastatic oral epithelial cells via various mechanisms including the promotion of migration, MMP activity or oncometabolite secretion. In this study, our findings demonstrate, that fungi-driven OSCC progression is also evident at the level of miRNA regulation, when C. albicans is present. In this context, the fungus might also enhance existing post-transcriptional regulatory mechanisms in the malignant oral epithelium. This behavior seems to be species-specific, as another common resident of the oral microflora, C. parapsilosis does not trigger such an effect.

microbiology↗

bioRxiv2023

Antibiotics of the future are prone to resistance in Gram-negative pathogens

Despite the ongoing development of new antibiotics, the future evolution of bacterial resistance may render them ineffective. We demonstrate that antibiotic candidates currently under development are as prone to resistance evolution in Gram-negative pathogens as clinically employed antibiotics. Resistance generally stems from both genomic mutations and the transfer of antibiotic resistance genes from microbiomes associated with humans, both factors carrying equal significance. The molecular mechanisms of resistance overlap with those found in commonly used antibiotics. Therefore, these mechanisms are already present in natural populations of pathogens, indicating that resistance can rapidly emerge through selection of pre-existing bacterial variants. However, certain combinations of antibiotics and bacterial strains are less prone to developing resistance, emphasizing the potential of narrow-spectrum antibacterial therapies that could remain effective. Our comprehensive framework allows for predicting future health risks associated with bacterial resistance to new antibiotics.

microbiology↗

bioRxiv2021

Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in {beta}-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates. Author summaryBenzene and its derivatives are simple aromatic compounds representing key substances for the chemical industry. While benzene itself is toxic and carcinogenic, benzoic acid is commonly used in the food industry and some of its derivatives are used in pharmacology (aspirin) or cosmetics (parabens). The benzene ring of aromatic molecules is relatively stable, but many microorganisms including yeasts break it enzymatically and, in a series of biochemical reactions, utilize resulting metabolites as carbon sources. Understanding the genetic basis of corresponding metabolic pathways and their regulation opens a venue for applications in biotechnology and bioremediation of polluted environments. Here we investigate the yeast Candida parapsilosis which assimilates various hydroxybenzenes and hydroxybenzoates via the 3-oxoadipate and gentisate pathways. We show that the genes coding for the substrate transporters and enzymes involved in both pathways are co-expressed and regulated by the transcriptional activators Otf1p and Gtf1p, respectively. Our results also reveal the connections of both pathways to central metabolism and organelle biogenesis and provide an insight into evolution of metabolism of hydroxyaromatic compounds.

genomics↗

bioRxiv2021

Nicotinate degradation in a microbial eukaryote: a novel, complete pathway extant in Aspergillus nidulans

Several strikingly different aerobic and anaerobic pathways of nicotinate utilization had been described in bacteria. No similar work is extant in any eukaryote. Here we elucidate a complete eukaryotic nicotinate utilization pathway, by constructing single or multiple gene deleted strains and identifying metabolic intermediates by ultra-high performance liquid chromatography - high-resolution mass spectrometry. Enzymes catalyzing each step and all intermediate metabolites were identified. We previously established that the cognate eleven genes organized in three clusters constitute a regulon, strictly dependent on HxnR, a pathway-specific transcription factor. The first step, hydroxylation of nicotinic acid to 6-hydroxynicotinic acid is analogous to that occurring in bacterial pathways and is catalyzed by an independently evolved molybdenum-containing hydroxylase. The following enzymatic steps have no prokaryotic equivalents: 6-hydroxynicotinic acid is converted to 2,3,6-trihydroxypyridine through 2,5-dihydroxypiridine and the trihydroxylated pyridine ring is then saturated to 5,6-dihydroxypiperidine-2-one followed by the oxidation of the C6 hydroxyl group resulting in 3-hydroxypiperidine-2,6-dione. The latter two heterocyclic compounds are newly identified cellular metabolites, while 5,6-dihydroxypiperidine-2-one is a completely new chemical compound. Ring opening between C and N results in -hydroxyglutaramate, an unprecedented compound in prokaryotic nicotinate catabolic routes. The pathway extant in A. nidulans, and in many other ascomycetes, is different from any other previously analyzed in bacteria. Our earlier phylogenetic analysis of Hxn proteins together with the complete novel biochemical pathway we now describe further illustrates the convergent evolution of catabolic pathways between fungi and bacteria. Significance StatementThis eukaryotic nicotinate catabolic pathway illustrates the convergent evolution of prokaryotic and microbial eukaryotic metabolism. It brings to light newly identified metabolites and step processing enzymes. The identification of hitherto undescribed metabolites - which could serve as precursor biosynthetic molecules - is potentially relevant to both pharmaceutical and agrochemical industries.

microbiology↗

bioRxiv2021

Candida albicans enhances the progression of oral squamous cell cancrinoma in vitro and in vivo

Oral squamous cell carcinoma (OSCC) is a serious health issue worldwide. OSCC is highly associated with oral candidiasis, although it is unclear whether the fungus promotes the genesis and progression of OSCC or cancer facilitates the growth of the fungus. Therefore, we investigated whether Candida could directly influence OSCC development and progression. Our in vitro results suggest that the presence of live C. albicans, but not C. parapsilosis, enhances the progression of OSCC by stimulating the production of matrix metalloproteinases, oncometabolites, pro-tumor signaling routes, and overexpression of prognostic marker genes associated with metastatic events. We also found that oral candidiasis triggered by C. albicans enhanced the progression of OSCC in vivo through the induction of inflammation and overexpression of metastatic genes and markers of epithelial-mesenchymal transition. Taken together, these results suggest that C. albicans actively participates in the complex process of OSCC progression.

microbiology↗

bioRxiv2021

Oral epithelial cells distinguish between Candida species with high or low pathogenic potential through miRNA regulation

Oral epithelial cells monitor microbiome composition and initiate immune response upon dysbiosis, as in case of Candida imbalances. Comparison of healthy oral epithelial cell responses revealed that the inability of C. parapsilosis to induce a robust antifungal response was due to activation of various inflammation-independent pathways, while C. albicans robustly activated inflammation cascades. Regarding posttranscriptional regulation, several miRNAs were altered by both species. For C. parapsilosis, the applied dose directly correlated with changes in transcriptomic responses. Carbohydrate metabolism, hypoxia- and cardiovascular development-related responses dominate after C. parapsilosis stimulus, whereas C. albicans altered inflammatory responses. Subsequent analyses of HIF1- and HSC-activation pathways predicted target genes through which miRNA-dependent regulation of yeast-specific functions may occur, supporting the observed responses. Thus, C. parapsilosis is recognized as a commensal at low doses by the oral epithelium; however, increased fungal burden activates different pathways, some of which overlap with inflammatory processes induced by C. albicans. Impact statementAltered miRNA regulation discriminates between C. albicans and C. parapsilosis in human oral epithelial cells

microbiology↗

bioRxiv2019

Phagocytic predation by the fungivorous amoeba Protostelium aurantium targets metal ion and redox homeostasis

Predatory interactions among microbes are considered to be a major evolutionary driving force for biodiversity and the defense against phagocytic killing. The fungivorous amoeba Protostelium aurantium has a wide fungal food spectrum but strongly discriminates among major pathogenic members of the Saccharomycotina. While C. albicans is not recognized, C. glabrata is rapidly internalized, but remains undigested. Phagocytic killing and feeding by P. aurantium is highly effective for the third major fungal pathogen, C. parapsilosis. Here we show that the different prey patterns of the three yeasts were reflected by distinct transcriptional responses, indicating fungal copper and redox homeostasis as primary targets during intracellular killing of C. parapsilosis. Gene deletions in this fungus for the highly expressed copper exporter Crp1 and the peroxiredoxin Prx1 confirmed their role in copper and redox homeostasis, respectively and identified methionine biosynthesis as a ROS sensitive metabolic target during predation. Both, intact Cu export and redox homeostasis contributed to the survival of C. parapsilosis not only when encountering P. aurantium, but also in the presence of human macrophages. As both genes were found to be widely conserved within the entire Candida clade, our results suggest that they could be part of a basic tool-kit to survive phagocytic attacks by environmental predators.

microbiology↗

bioRxiv2019

Candida auris: multi-omics signature of an emerging and multidrug-resistant pathogen

Candida auris is a recently described pathogenic fungus that is causing invasive outbreaks on all continents. The fungus is of high concern given the numbers of multidrug-resistant strains that have been isolated in distinct sites across the globe. The fact that its diagnosis is still problematic suggests that the spreading of the pathogen remains underestimated. Notably, the molecular mechanisms of virulence and antifungal resistance employed by this new species are largely unknown. In the present work, we compared two clinical isolates of C. auris with distinct drug susceptibility profiles and a Candida albicans reference strain using a multi-omics approach. Our results show that, despite the distinct drug-resistance profile, both C. auris strains appear to be very similar, albeit with a few notable differences. However, when compared to C. albicans both C. auris strains have major differences regarding their carbon utilization and downstream lipid and protein content, suggesting a multi-factorial mechanism of drug resistance. The molecular profile displayed by C. auris helps to explain the antifungal resistance and virulence phenotypes of this new emerging pathogen. ImportanceCandida auris was firstly described in Japan in 2009 and has now been the cause of significant outbreaks across the globe. The high number of isolates that are resistant to one or more antifungals, as well as the high mortality rates from patients with bloodstream infections, has caught the attention of the medical mycology, infectious disease and public health communities to this pathogenic fungus. In the current work, we performed a broad multi-omics approach on two clinical isolates isolated in New York, the most affected area in the USA and found that the omic profile of C. auris differs significantly from C. albicans. Besides our insights into C. auris carbon utilization and lipid and protein content, we believe that the availability of these data will enhance our ability to combat this rapidly emerging pathogenic yeast.

microbiology↗