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Cowen, L. E.

Publications and source records attributed to Cowen, L. E..

10 recordsLinked to original sources

Extracellular vesicle packaging of a supercluster-encoded antimicrobial combination with enhanced potency against fungal biofilms

Bacterial specialized metabolites are bioactive compounds that have been mined extensively as antibacterials, antifungals, and other drugs. They are widely used as experimental probes of complex biological systems. Since their discovery, their functional characteristics have typically been investigated as single, soluble compounds. The discoveries in this work expand this model. First, we report the co-packaging in extracellular vesicles (EVs) of two specialized metabolite complexes, candicidin and antimycin A, the products of a supercluster of biosynthetic genes, by a Streptomyces soil isolate. Secondly, we report that the products of this supercluster have synergistic antimicrobial activity against fungal biofilms, whereas biofilms are tolerant to the individual compounds. Finally, we show that co-packaging these compounds in EVs ensures simultaneous delivery with enhanced potency. This research advances understanding of the elegant complexity that shapes the evolution and function of bacterial specialized metabolites. In particular, the enhanced antibiofilm activity of co-packaged metabolites compared to individual soluble compounds is notable given the relevance of biofilms to microbial ecology and to pathogenesis. Our work supports the evolution of coordinated activity of specialized metabolites to counter conditional environmental challenges, and highlights co-packaging in EVs as one mechanism for secretion and co-delivery of combinations of bioactive molecules.

microbiology↗

Dna2-intrinsic condensation regulates DNA end resection and reveals evolutionary redistribution of condensate grammar

Eukaryotic cells commonly use biomolecular condensation of DNA double-strand break (DSB) repair scaffolds and signaling assemblies to organize repair reactions in space and time. Yet whether DSB end-processing enzymes themselves encode tunable phase separation that potentiates resection remains unclear. Here we show that the long-range resection enzyme Dna2 forms liquid-like condensates through an intrinsically disordered region that is necessary and sufficient for phase separation and catalytic enhancement in Saccharomyces cerevisiae. Dna2 condensates concentrate DNA substrates and enhance end processing, whereas disrupting condensate formation impairs repair kinetics, checkpoint signaling, and chromosome stability. Grafting of the heterologous intrinsically disordered region of human FUS partly rescues condensate formation and function, and Cdk1-dependent phosphorylation sites tune condensate stability and enzymatic output in cis and in trans. Machine-learning-based analysis reveals that condensation-promoting features of fungal Dna2 are shared with a restricted set of human DNA2-associated resection regulators. Together, these findings define phosphorylation-tuned, enzyme-intrinsic phase separation as an organizational principle of DSB end resection while supporting a model in which condensation-promoting features are redistributed among factors operating within conserved genome maintenance pathways.

molecular biology↗

Structure-activity Relationship for Diarylpyrazoles as Inhibitors of the Fungal Kinase Yck2

Candida albicans is a growing global health threat, causing 1.5 million invasive infections and 1 million deaths annually. Yeast casein kinase 2 (Yck2) in C. albicans has emerged as an antifungal target of the kinase inhibitor LY364947 (LY). Herein, we report Yck2 structure-activity relationships for 3,4- and 3,4,5-substituted pyrazole analogs of LY. X-ray crystallography and in vitro profiling revealed the importance of the hinge-binding heterocycle for Yck2 inhibition and fungal kinome selectivity. A hydrogen-bond network between the inhibitor, a bound water molecule, and catalytic residues within the ATP pocket was identified as a key determinant of selectivity over other fungal and human kinases. Phenol analog 11 showed remarkable selectivity for Yck2 and Yck22 over all other C. albicans protein kinases. Several of the LY analogs, including 11, demonstrated improved antifungal activity. These findings provide a framework for translating human kinase inhibitors into highly selective antifungal Yck2 inhibitors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/664496v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@ef6a04org.highwire.dtl.DTLVardef@193b73org.highwire.dtl.DTLVardef@8e109corg.highwire.dtl.DTLVardef@e4a243_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Chemoproteomic Profiling of C. albicans for Characterization of Anti-fungal Kinase Inhibitors

Candida albicans is a growing health concern as the leading causal agent of systemic candidiasis, a life-threatening fungal infection with a mortality rate of [~]40% despite best available therapy. Yck2, a fungal casein kinase 1 (CK1) family member, is the cellular target of inhibitors YK-I-02 (YK) and MN-I-157 (MN). Here, multiplexed inhibitor beads paired with mass spectrometry (MIB/MS) employing ATP-competitive kinase inhibitors were used to define the selectivity of these Yck2 inhibitors across the global C. albicans proteome. The MIB matrix captured 89% of the known and predicted C. albicans protein kinases present in cell lysate. In MIB/MS competition assays, YK and MN demonstrated exquisite selectivity across the C. albicans fungal kinome with target engagement of only three CK1 homologs (Yck2, Yck22, and Hrr25) and a homolog of human p38 (Hog1). Additional chemoproteomics using a custom MN-kinobead identified only one additional C. albicans protein, confirming its remarkable fungal proteome-wide selectivity. To identify new Yck2 inhibitors with selectivity over Hog1, thirteen human CK1 kinase inhibitors were profiled for fungal kinase-binding activity using MIB/MS competition assays and in-cell NanoBRET target engagement assays. A new chemotype of family-selective Yck2 inhibitors with antifungal activity was identified. Together, these findings expand the application of MIB/MS proteomic profiling for non-human kinomes and demonstrate its utility in the discovery and development of selective inhibitors of fungal kinases with potential antimicrobial activity. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/632200v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1606f86org.highwire.dtl.DTLVardef@39c92borg.highwire.dtl.DTLVardef@1c666cborg.highwire.dtl.DTLVardef@869b5c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Butyrolactol A is a phospholipid flippase inhibitor that potentiates the bioactivity of caspofungin against resistant fungi

Fungal infections cause millions of deaths annually and are challenging to treat due to limited therapeutic options and rising resistance. Cryptococci are intrinsically resistant to the latest generation of antifungals, echinocandins, while Candida auris, a notorious global threat, is also increasingly resistant. We performed a natural product extract screen to rescue caspofungin fungicidal activity against Cryptococcus neoformans H99 and identified butyrolactol A, which restores echinocandin efficacy against resistant fungal pathogens, including multidrug-resistant C. auris. Mode of action studies revealed that butyrolactol A inhibits the phospholipid flippase Apt1-Cdc50, blocking phospholipid transport. Cryo-electron microscopy analysis of the Apt1*butyrolactol A complex revealed that the flippase is trapped in a dead-end state. Apt1 inhibition disrupts membrane asymmetry, vesicular trafficking, and cytoskeletal organization, thereby enhancing echinocandin uptake and potency. This study identifies lipid flippases as promising antifungal targets and demonstrates the potential of revisiting natural products to expand the antifungal arsenal and combat resistance.

biochemistry↗

Adaptation of the tetracycline-repressible system for modulating the expression of essential genes in Cryptococcus neoformans

The opportunistic human fungal pathogen Cryptococcus neoformans has an enormous impact on human health as the causative agent of cryptococcal meningitis, an AIDS-defining illness that results in significant human mortality. To combat C. neoformans infections, there is a dire need to expand our current antifungal arsenal. Essential gene products often serve as ideal targets for antimicrobials, and thus identifying and characterizing essential genes in a pathogen of interest is critical for drug development. Unfortunately, characterization of essential genes in C. neoformans is limited due to its haploid nature and lack of genetic tools for generating effective conditional-expression mutants. To date, the copper-repressible promoter pCTR4 is the mostly widely used system to regulate essential gene expression, however, its expression is leaky and copper has pleiotropic effects. In diverse fungal species, including Saccharomyces cerevisiae, Candida albicans, and Candida auris, the tetracycline-repressible promoter system is a powerful tool to regulate gene expression, however, it has yet to be adapted for C. neoformans. In this study, we successfully implemented the tetracycline-repressible system in C. neoformans to regulate the expression of the essential gene HSP90. Supplementation of cultures with the tetracycline analog doxycycline efficiently depleted HSP90 at both transcript and protein levels and inhibited C. neoformans growth and viability. Thus, this work unveils a novel approach to generate conditional-expression mutants in C. neoformans, providing unprecedented potential to systematically study essential gene function in this important human fungal pathogen.

molecular biology↗

The Cryptococcus neoformans STRIPAK complex controls genome stability, sexual development, and virulence

The eukaryotic serine/threonine protein phosphatase PP2A is a heterotrimeric enzyme composed of a scaffold A subunit, a regulatory B subunit, and a catalytic C subunit. Of the four known B subunits, the B subunit (known as striatin) interacts with the multi-protein striatin-interacting phosphatase and kinase (STRIPAK) complex. Orthologs of STRIPAK components were identified in Cryptococcus neoformans, namely PP2AA/Tpd3, PP2AC/Pph22, PP2AB/Far8, STRIP/Far11, SLMAP/Far9, and Mob3. Structural modeling, protein domain analysis, and detected protein-protein interactions suggest C. neoformans STRIPAK is assembled similarly to the human and fungal orthologs. Here, STRIPAK components Pph22, Far8, and Mob3 were functionally characterized. Whole-genome sequencing revealed that mutations in STRIPAK complex subunits lead to increased segmental and chromosomal aneuploidy, suggesting STRIPAK functions in maintaining genome stability. We demonstrate that PPH22 is a haploinsufficient gene: heterozygous PPH22/pph22{Delta} mutant diploid strains exhibit defects in hyphal growth and sporulation and have a significant fitness disadvantage when grown in competition against a wild-type diploid. Deletion mutants pph22{Delta}, far8{Delta}, and mob3{Delta} exhibit defects in mating and sexual differentiation, including impaired hyphae, basidia, and basidiospore production. Loss of either PPH22 or FAR8 in a haploid background leads to growth defects at 30C, severely reduced growth at elevated temperature, abnormal cell morphology, and impaired virulence. Additionally, pph22{Delta} strains frequently accumulate suppressor mutations that result in overexpression of another putative PP2A catalytic subunit, PPG1. The pph22{Delta} and far8{Delta} mutants are also unable to grow in the presence of the calcineurin inhibitors cyclosporine A or FK506, and thus these mutations are synthetically lethal with loss of calcineurin activity. Conversely, mob3{Delta} mutants display increased thermotolerance, capsule production, and melanization, and are hypervirulent in a murine infection model. Taken together, these findings reveal that the C. neoformans STRIPAK complex plays an important role in genome stability, vegetative growth, sexual development, and virulence in this prominent human fungal pathogen. Author summaryThis study focused on a highly conserved protein signaling complex known as STRIPAK, which is important for various developmental processes in fungi and humans. By investigating the functions of this complex in Cryptococcus neoformans, it was discovered to play crucial roles in maintaining genome stability, sexual development, and pathogenesis. In particular, mutations in the genes encoding two subunits of the STRIPAK complex were found to lead to significant defects, including abnormal growth and cell morphology, compromised stress response, and impaired virulence. Interestingly, mutation of a third STRIPAK complex subunit resulted in hypervirulence, characterized by increased thermotolerance, enhanced production of melanin pigment and polysaccharide capsule, and reduced survival in infected animals. Our findings reveal that the STRIPAK complex is an important regulator of growth and virulence of C. neoformans, highlighting its potential as a target for therapies aimed at combating fungal infections. This work furthers understanding of how the STRIPAK complex functions in Cryptococcus, and also in other organisms including humans, where related protein phosphatase complexes govern key cellular processes.

microbiology↗

Deep tissue infection by an invasive human fungal pathogen requires novel lipid-based suppression of the IL-17 response

Candida albicans is the most common cause of human fungal infection, but the mechanisms of invasive pathogenesis remain poorly defined. Here we identify an unexpected mechanism: lipid-mediated immunosuppression. Through forward genetics, we found that C. albicans secretes a lipase, Lip2, that is critical for invasive disease. Murine infection with C. albicans strains that lack Lip2 display an exaggerated host IL-17 response that leads to fungal clearance from solid organs and host survival. IL-17 signaling is required for Lip2 action. The lipase activity of Lip2 inhibits IL-17 production indirectly through suppression of IL-23 production by tissue resident dendritic cells. We conclude that C. albicans suppresses antifungal IL-17 defense in solid organs by altering the tissue lipid milieu.

microbiology↗

Defining the Yeast Resistome through in vitro Evolution and Whole Genome Sequencing

In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in the model microbe, Saccharomyces cerevisiae. Analysis of 355 curated, laboratory-evolved clones, resistant to 80 different compounds, demonstrates differences in the types of mutations that are identified in selected versus neutral evolution and reveals numerous new, compound-target interactions. Through enrichment analysis we further identify a set of 137 genes strongly associated with or conferring drug resistance as indicated by CRISPR-Cas9 engineering. The set of 25 most frequently mutated genes was enriched for transcription factors and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function, single nucleotide variants found in 170-amino-acid domains in two Zn2C6 transcription factors, YRR1 and YRM1 (p < 1x 10 -100). This remarkable enrichment for transcription factors as drug resistance genes may explain why it is challenging to develop effective antifungal killing agents and highlights their important role in evolution.

genetics↗

Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase

During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.

biophysics↗