High-Throughput Profiling of Candida auris Isolates Reveals Clade-Specific Metabolic Differences.

Candida auris, a multidrug-resistant human fungal pathogen that causes outbreaks of invasive infections, emerged as four distinct geographical clades. Previous studies identified genomic and proteomic differences in nutrient utilization on comparison to Candida albicans, suggesting that certain metabolic features may contribute to C. auris emergence. Since no high-throughput clade-specific metabolic characterization has been described yet, we performed a phenotypic screening of C. auris strains from all 4 clades on 664 nutrients, 120 chemicals, and 24 stressors. We identified common and clade- or strain-specific responses, including the preferred utilization of various dipeptides as nitrogen source and the inability of the clade II isolate AR 0381 to withstand chemical stress. Further analysis of the metabolic properties of C. auris isolates showed robust growth on intermediates of the tricarboxylic acid cycle, such as citrate and succinic and malic acids. However, there was reduced or no growth on pyruvate, lactic acid, or acetate, likely due to the lack of the monocarboxylic acid transporter Jen1, which is conserved in most pathogenic Candida species. Comparison of C. auris and C. albicans transcriptomes of cells grown on alternative carbon sources and dipeptides as a nitrogen source revealed common as well as species-unique responses. C. auris induced a significant number of genes with no ortholog in C. albicans, e.g., genes similar to the nicotinic acid transporter TNA1 (alternative carbon sources) and to the oligopeptide transporter (OPT) family (dipeptides). Thus, C. auris possesses unique metabolic features which could have contributed to its emergence as a pathogen. IMPORTANCE Four main clades of the emerging, multidrug-resistant human pathogen Candida auris have been identified, and they differ in their susceptibilities to antifungals and disinfectants. Moreover, clade- and strain-specific metabolic differences have been identified, but a comprehensive overview of nutritional characteristics and resistance to various stressors is missing. Here, we performed high-throughput phenotypic characterization of C. auris on various nutrients, stressors, and chemicals and obtained transcriptomes of cells grown on selected nutrients. The generated data sets identified multiple clade- and strain-specific phenotypes and induction of C. auris-specific metabolic genes, showing unique metabolic properties. The presented work provides a large amount of information for further investigations that could explain the role of metabolism in emergence and pathogenicity of this multidrug-resistant fungus.

Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans.

Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.

Candida albicans SR-Like Protein Kinases Regulate Different Cellular Processes: Sky1 Is Involved in Control of Ion Homeostasis, While Sky2 Is Important for Dipeptide Utilization.

Protein kinases play a crucial role in regulating cellular processes such as growth, proliferation, environmental adaptation and stress responses. Serine-arginine (SR) protein kinases are highly conserved in eukaryotes and regulate fundamental processes such as constitutive and alternative splicing, mRNA processing and ion homeostasis. The Candida albicans genome encodes two (Sky1, Sky2) and the Candida glabrata genome has one homolog (Sky1) of the human SR protein kinase 1, but their functions have not yet been investigated. We used deletion strains of the corresponding genes in both fungi to study their cellular functions. C. glabrata and C. albicans strains lacking SKY1 exhibited higher resistance to osmotic stress and toxic polyamine concentrations, similar to Saccharomyces cerevisiae sky1Δ mutants. Deletion of SKY2 in C. albicans resulted in impaired utilization of various dipeptides as the sole nitrogen source. Subsequent phosphoproteomic analysis identified the di- and tripeptide transporter Ptr22 as a potential Sky2 substrate. Sky2 seems to be involved in Ptr22 regulation since overexpression of PTR22 in the sky2Δ mutant restored the ability to grow on dipeptides and made the cells more susceptible to the dipeptide antifungals Polyoxin D and Nikkomycin Z. Altogether, our results demonstrate that C. albicans and C. glabrata Sky1 protein kinases are functionally similar to Sky1 in S. cerevisiae, whereas C. albicans Sky2, a unique kinase of the CTG clade, likely regulates dipeptide uptake via Ptr22.

GNP2 Encodes a High-Specificity Proline Permease in Candida albicans.

The tight association of Candida albicans with the human host has driven the evolution of mechanisms that permit metabolic flexibility. Amino acids, present in a free or peptide-bound form, are abundant carbon and nitrogen sources in many host niches. In C. albicans, the capacity to utilize certain amino acids, like proline, is directly connected to fungal morphogenesis and virulence. Yet the precise nature of proline sensing and uptake in this pathogenic fungus has not been investigated. Since C. albicans encodes 10 putative orthologs of the four Saccharomyces cerevisiae proline transporters, we tested deletion strains of the respective genes and identified Gnp2 (CR_09920W) as the main C. albicans proline permease. In addition, we found that this specialization of Gnp2 was reflected in its transcriptional regulation and further assigned distinct substrate specificities for the other orthologs, indicating functional differences of the C. albicans amino acid permeases compared to the model yeast. The physiological relevance of proline uptake is exemplified by the findings that strains lacking GNP2 were unable to filament in response to extracellular proline and had a reduced capacity to damage macrophages and impaired survival following phagocytosis. Furthermore, GNP2 deletion rendered the cells more sensitive to oxidative stress, illustrating new connections between amino acid uptake and stress adaptation in C. albicans. IMPORTANCE The utilization of various nutrients is of paramount importance for the ability of Candida albicans to successfully colonize and infect diverse host niches. In this context, amino acids are of special interest due to their ubiquitous availability, relevance for fungal growth, and direct influence on virulence traits like filamentation. In this study, we identify a specialized proline transporter in C. albicans encoded by GNP2. The corresponding amino acid permease is essential for proline-induced filamentation, oxidative stress resistance, and fungal survival following interaction with macrophages. Altogether, this work highlights the importance of amino acid uptake for metabolic and stress adaptation in this fungus.

Cucurbit[6]uril@MIL-101-Cl: loading polar porous cages in mesoporous stable host for enhanced SO2 adsorption at low pressures.

The robust cucurbituril-MOF composite CB6@MIL-101-Cl was synthesized by a wet impregnation method and a concomitant OH-to-Cl ligand exchange {CB6 = cucurbit[6]uril, 31 wt% content in the composite, MIL-101-Cl = [Cr3(O)Cl(H2O)2(BDC)3], BDC = benzene-1,4-dicarboxylate}. MIL-101-Cl was formed postsynthetically from standard fluorine-free MIL-101 where Cr-OH ligands were substituted by Cl during treatment with HCl. CB6@MIL-101-Cl combines the strong SO2 affinity of the rigid CB6 macrocycles and the high SO2 uptake capacity of MIL-101, and shows a high SO2 uptake of 438 cm3 g-1 (19.5 mmol g-1) at 1 bar and 293 K (380 cm3 g-1, 17.0 mmol g-1 at 1 bar and 298 K). The captured SO2 amount is 2.2 mmol g-1 for CB6@MIL-101-Cl at 0.01 bar and 293 K (2.0 mmol g-1 at 298 K), which is three times higher than that of the parent MIL-101 (0.7 mmol g-1) under the same conditions. The near zero-coverage SO2 adsorption enthalpies of MIL-101 and CB6@MIL-101-Cl are -35 kJ mol-1 and -50 kJ mol-1, respectively, reflecting the impact of the incorporated CB6 macrocycles, having higher affinity towards SO2. FT-IR spectroscopy confirms the interactions of the SO2 with the cucurbit[6]uril moieties of the CB6@MIL-101-Cl composite and SO2 retention for a few minutes under ambient air. Comparative experiments demonstrated loss of crystallinity and porosity after dry SO2 adsorption for MIL-101, while CB6@MIL-101-Cl exhibits nearly complete retention of crystallinity and porosity under the exposure to both dry and wet SO2. Thus, CB6@MIL-101-Cl can be an attractive adsorbent for SO2 capture because of its excellent recycling stability, high capacity and strong affinity toward SO2 at low pressure.

Capture and Separation of SO2 Traces in Metal-Organic Frameworks via Pre-Synthetic Pore Environment Tailoring by Methyl Groups.

Herein, we report a pre-synthetic pore environment design strategy to achieve stable methyl-functionalized metal-organic frameworks (MOFs) for preferential SO2 binding and thus enhanced low (partial) pressure SO2 adsorption and SO2 /CO2 separation. The enhanced sorption performance is for the first time attributed to an optimal pore size by increasing methyl group densities at the benzenedicarboxylate linker in [Ni2 (BDC-X)2 DABCO] (BDC-X=mono-, di-, and tetramethyl-1,4-benzenedicarboxylate/terephthalate; DABCO=1,4-diazabicyclo[2,2,2]octane). Monte Carlo simulations and first-principles density functional theory (DFT) calculations demonstrate the key role of methyl groups within the pore surface on the preferential SO2 affinity over the parent MOF. The SO2 separation potential by methyl-functionalized MOFs has been validated by gas sorption isotherms, ideal adsorbed solution theory calculations, simulated and experimental breakthrough curves, and DFT calculations.

Zirconium and Aluminum MOFs for Low-Pressure SO2 Adsorption and Potential Separation: Elucidating the Effect of Small Pores and NH2 Groups.

Finding new adsorbents for the desulfurization of flue gases is a challenging task but is of current interest, as even low SO2 emissions impair the environment and health. Four Zr- and eight Al-MOFs (Zr-Fum, DUT-67(Zr), NU-1000, MOF-808, Al-Fum, MIL-53(Al), NH2-MIL-53(Al), MIL-53(tdc)(Al), CAU-10-H, MIL-96(Al), MIL-100(Al), NH2-MIL-101(Al)) were examined toward their SO2 sorption capability. Pore sizes in the range of about 4-8 Å are optimal for SO2 uptake in the low-pressure range (up to 0.1 bar). Pore widths that are only slightly larger than the kinetic diameter of 4.1 Å of the SO2 molecules allow for multi-side-dispersive interactions, which translate into high affinity at low pressure. Frameworks NH2-MIL-53(Al) and NH2-MIL-101(Al) with an NH2-group at the linker tend to show enhanced SO2 affinity. Moreover, from single-gas adsorption isotherms, ideal adsorbed solution theory (IAST) selectivities toward binary SO2/CO2 gas mixtures were determined with selectivity values between 35 and 53 at a molar fraction of 0.01 SO2 (10.000 ppm) and 1 bar for the frameworks Zr-Fum, MOF-808, NH2-MIL-53(Al), and Al-Fum. Stability tests with exposure to dry SO2 during ≤10 h and humid SO2 during 5 h showed full retention of crystallinity and porosity for Zr-Fum and DUT-67(Zr). However, NU-1000, MOF-808, Al-Fum, MIL-53(tdc), CAU-10-H, and MIL-100(Al) exhibited ≥50-90% retained Brunauer-Emmett-Teller (BET)-surface area and pore volume; while NH2-MIL-100(Al) and MIL-96(Al) demonstrated a major loss of porosity under dry SO2 and MIL-53(Al) and NH2-MIL-53(Al) under humid SO2. SO2 binding sites were revealed by density functional theory (DFT) simulation calculations with adsorption energies of -40 to -50 kJ·mol-1 for Zr-Fum and Al-Fum and even above -50 kJ·mol-1 for NH2-MIL-53(Al), in agreement with the isosteric heat of adsorption near zero coverage (ΔHads0). The predominant, highest binding energy noncovalent binding modes in both Zr-Fum and Al-Fum feature µ-OHδ+···Î´-OSO hydrogen bonding interactions. The small pores of Al-Fum allow the interaction of two µ-OH bridges from opposite pore walls with the same SO2 molecule via OHδ+···Î´-OSOδ-···Î´+HO hydrogen bonds. For NH2-MIL-53(Al), the DFT high-energy binding sites involve NHδ+···Î´-OS together with the also present Al-µ-OHδ+···Î´-OS hydrogen bonding interactions and C6-πδ-···Î´+SO2, Nδ-···Î´+SO2 interactions.

Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.

Candida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants of fungal abundance. We optimized the predictive capacity of our model using wild type and mutant C. albicans growth data and used it for in silico metabolic interaction predictions. Our analysis of more than 900 paired fungal-bacterial metabolic models predicted key gut bacterial species modulating C. albicans colonization levels. Among the studied microbes, Alistipes putredinis was predicted to negatively affect C. albicans levels. We confirmed these findings by metagenomic sequencing of stool samples from 24 human subjects and by fungal growth experiments in bacterial spent media. Furthermore, our pairwise simulations guided us to specific metabolites with promoting or inhibitory effect to the fungus when exposed in defined media under carbon and nitrogen limitation. Our study demonstrates that in silico metabolic prediction can lead to the identification of gut microbiome features that can significantly affect potentially harmful levels of C. albicans.

Clinical Candida albicans Vaginal Isolates and a Laboratory Strain Show Divergent Behaviors during Macrophage Interactions.

Typically, established lab strains are widely used to study host-pathogen interactions. However, to better reflect the infection process, the experimental use of clinical isolates has come more into focus. Here, we analyzed the interaction of multiple vaginal isolates of the opportunistic fungal pathogen Candida albicans, the most common cause of vulvovaginal candidiasis in women, with key players of the host immune system: macrophages. We tested several strains isolated from asymptomatic or symptomatic women with acute and recurrent infections. While all clinical strains showed a response similar to the commonly used lab strain SC5314 in various in vitro assays, they displayed remarkable differences during interaction with macrophages. This coincided with significantly reduced ß-glucan exposure on the cell surface, which appeared to be a shared property among the tested vaginal strains for yeast extract/peptone/dextrose-grown cells, which is partly lost when the isolates faced vaginal niche-like nutrient conditions. However, macrophage damage, survival of phagocytosis, and filamentation capacities were highly strain-specific. These results highlight the high heterogeneity of C. albicans strains in host-pathogen interactions, which have to be taken into account to bridge the gap between laboratory-gained data and disease-related outcomes in an actual patient.IMPORTANCE Vulvovaginal candidiasis is one of the most common fungal infections in humans with Candida albicans as the major causative agent. This study is the first to compare clinical vaginal isolates of defined patient groups in their interaction with macrophages, highlighting the vastly different outcomes in comparison to a laboratory strain using commonly applied virulence-determining assays.

The Transcription Factor Stp2 Is Important for Candida albicans Biofilm Establishment and Sustainability.

The fungal pathogen Candida albicans forms polymorphic biofilms where hyphal morphogenesis and metabolic adaptation are tightly coordinated by a complex intertwined network of transcription factors. The sensing and metabolism of amino acids play important roles during various phases of biofilm development - from adhesion to maturation. Stp2 is a transcription factor that activates the expression of amino acid permease genes and is required for environmental alkalinization and hyphal growth in vitro and during macrophage phagocytosis. While it is well established that Stp2 is activated in response to external amino acids, its role in biofilm formation remains unknown. In addition to widely used techniques, we applied newly developed approaches for automated image analysis to quantify Stp2-regulated filamentation and biofilm growth. Our results show that in the stp2Δ deletion mutant adherence to abiotic surfaces and initial germ tube formation were strongly impaired, but formed mature biofilms with cell density and morphological structures comparable to the control strains. Stp2-dependent nutrient adaptation appeared to play an important role in biofilm development: stp2Δ biofilms formed under continuous nutrient flow displayed an overall reduction in biofilm formation, whereas under steady conditions the mutant strain formed biofilms with lower metabolic activity, resulting in increased cell survival and biofilm longevity. A deletion of STP2 led to increased rapamycin susceptibility and transcriptional activation of GCN4, the transcriptional regulator of the general amino acid control pathway, demonstrating a connection of Stp2 to other nutrient-responsive pathways. In summary, the transcription factor Stp2 is important for C. albicans biofilm formation, where it contributes to adherence and induction of morphogenesis, and mediates nutrient adaption and cell longevity in mature biofilms.

Encapsulation of Phosphorescent Pt(II) Complexes in Zn-Based Metal-Organic Frameworks toward Oxygen-Sensing Porous Materials.

In this work, we synthesized two tailored phosphorescent Pt(II) complexes bearing a cyclometalating tridentate thiazole-based C^N*N pincer luminophore (L) and exchangeable chlorido ([PtCl(L)]) or cyanido ([PtCN(L)]) coligands. While both complexes showed photoluminescence from metal-perturbed ligand-centered triplet states (3MP-LC), [PtCN(L)] reached the highest phosphorescence quantum yields and displayed a significant sensitivity toward quenching by 3O2. We encapsulated them into two Zn-based metal-organic frameworks, namely, MOF-5 and ZIF-8. The incorporation of the organometallic compounds in the resulting composites [PtCl(L)]@ZIF-8, [PtCN(L)]@ZIF-8, [PtCl(L)]@MOF-5, and [PtCN(L)]@MOF-5 was verified by powder X-ray diffractometry, scanning electron microscopy, time-resolved photoluminescence spectroscopy and microscopy, as well as N2- and Ar-gas sorption studies. The amount of encapsulated complex was determined by graphite furnace atomic absorption spectroscopy, showing a maximum loading of 3.7 wt %. If compared with their solid state forms, the solid-solution composites showed prolonged 3O2-sensitive excited state lifetimes for the complexes at room temperature, reaching up to 18.4 µs under an Ar atmosphere, which is comparable with the behavior of the complex in liquid solutions or even frozen glassy matrices at 77 K.

Metal-Organic Frameworks with Potential Application for SO2 Separation and Flue Gas Desulfurization.

Sulfur dioxide (SO2) is an acidic and toxic gas and its emission from utilizing energy from fossil fuels or in industrial processes harms human health and environment. Therefore, it is of great interest to find new materials for SO2 sorption to improve classic flue gas desulfurization. In this work, we present SO2 sorption studies for the three different metal-organic frameworks MOF-177, NH2-MIL-125(Ti), and MIL-160. MOF-177 revealed a new record high SO2 uptake (25.7 mmol·g-1 at 293 K and 1 bar). Both NH2-MIL-125(Ti) and MIL-160 show particular high SO2 uptakes at low pressures ( p < 0.01 bar) and thus are interesting candidates for the removal of remaining SO2 traces below 500 ppm from flue gas mixtures. The aluminum furandicarboxylate MOF MIL-160 is the most promising material, especially under application-orientated conditions, and features excellent ideal adsorbed solution theory selectivities (124-128 at 293 K, 1 bar; 79-95 at 353 K, 1 bar) and breakthrough performance with high onset time, combined with high stability under both humid and dry SO2 exposure. The outstanding sorption capability of MIL-160 could be explained by DFT simulation calculations and matching heat of adsorption for the binding sites Ofuran···SSO2 and OHAl-chain···OSO2 (both ∼40 kJ·mol-1) and Ofuran/carboxylate···SSO2 (∼55-60 kJ·mol-1).

Candida albicans responds to glycostructure damage by Ace2-mediated feedback regulation of Cek1 signaling.

Candida albicans uses the Cek1 MAPK pathway to restore cells from damage of its cell wall glycostructures. Defective protein N- or O-glycosylation activates Cek1 and the transcription factor Ace2 as its downstream target, to upregulate genes encoding protein O-mannosyltransferases (Pmt proteins). In unstressed cells, Cek1-Ace2 activity blocks expression of PMT1, which is de-repressed by tunicamycin. Genomic binding targets of Ace2 included ZCF21, which was upregulated by Ace2 and found to repress PMT1 transcription in unstressed cells. Surprisingly, genes encoding components of the Cek1 pathway including MSB2, CST20, HST7, CEK1 and ACE2 were also identified as Ace2 targets indicating Ace2-mediated transcriptional amplification of pathway genes under N-glycosylation stress. In this condition, physical interaction of the Ace2 protein with the upstream MAPKKK Cst20 was detected. Cst20-GFP showed stress-induced import from the cytoplasm into the nucleus and phosphorylation of Ace2. Interestingly, forced nuclear localization of Cst20 inhibited Cek1-Ace2 signaling, while forced cytoplasmic localization of Cst20 retained full signaling activity, suggesting that nuclear Cst20 downregulates the Cek1 pathway. Collectively, the results indicate that Ace2 is a versatile multifunctional transcriptional regulator, which activates glycostress responses of C. albicans by both positive forward and negative feedback regulation of Cek1 signaling.