Shared metabolism between a bacterial and fungal species that reside in the human gut.

The fungal species and the bacterium are members of the human gut microbiome. To explore the range of interactions between these two species, we utilized dual RNA-sequencing to transcriptionally profile both and during coculture (compared with monoculture controls) under two conditions: 1) an in vitro setting that mimics certain features of the gut environment and 2) a gnotobiotic mouse gut model. RNA-seq analysis revealed a large number of gene expression changes induced by one species in the presence of the other.

Variation in transcription regulator expression underlies differences in white-opaque switching between the SC5314 reference strain and the majority of Candida albicans clinical isolates.

Candida albicans, a normal member of the human microbiome and an opportunistic fungal pathogen, undergoes several morphological transitions. One of these transitions is white-opaque switching, where C. albicans alternates between 2 stable cell types with distinct cellular and colony morphologies, metabolic preferences, mating abilities, and interactions with the innate immune system.

Broad susceptibility of strains to 8-hydroxyquinolines and mechanisms of resistance.

The fungal pathogen represents a severe threat to hospitalized patients. Its resistance to multiple classes of antifungal drugs and ability to spread and resist decontamination in healthcare settings make it especially dangerous. We screened 1,990 clinically approved and late-stage investigational compounds for the potential to be repurposed as antifungal drugs targeting and narrowed our focus to five Food and Drug Administration (FDA)-approved compounds with inhibitory concentrations under 10 µM for and significantly lower toxicity to three human cell lines.

Ancient transcriptional regulators can easily evolve new pair-wise cooperativity.

Cells regulate gene expression by the specific binding of transcription regulators to cis-regulatory sequences. Pair-wise cooperativity between regulators-whereby two different regulators physically interact and bind DNA in a cooperative manner-is common and permits complex modes of gene regulation. Over evolutionary timescales, the formation of new combinations of regulators represents a major source of phenotypic novelty, facilitating new network structures.

Cell-type memory in a single-cell eukaryote requires the continuous presence of a specific transcription regulator.

A fundamental question in biology is how a eukaryotic cell type can be stably maintained through many rounds of DNA replication and cell division. In this paper, we investigate this question in a fungal species, , where two different cells types (white and opaque) arise from the same genome. Once formed, each cell type is stable for thousands of generations.

Evolution of a new form of haploid-specific gene regulation appearing in a limited clade of ascomycete yeast species.

Over evolutionary timescales, the logic and pattern of cell-type specific gene expression can remain constant, yet the molecular mechanisms underlying such regulation can drift between alternative forms. Here, we document a new example of this principle in the regulation of the haploid-specific genes in a small clade of fungal species. For most ascomycete fungal species, transcription of these genes is repressed in the a/α cell type by a heterodimer of two homeodomain proteins, Mata1 and Matα2.

Broad sensitivity of strains to quinolones and mechanisms of resistance.

Unlabelled: The fungal pathogen represents a severe threat to hospitalized patients. Its resistance to multiple classes of antifungal drugs and ability to spread and resist decontamination in health-care settings make it especially dangerous. We screened 1,990 clinically approved and late-stage investigational compounds for the potential to be repurposed as antifungal drugs targeting and narrowed our focus to five FDA-approved compounds with inhibitory concentrations under 10 µM for and significantly lower toxicity to three human cell lines.

Farnesol and phosphorylation of the transcriptional regulator Efg1 affect Candida albicans white-opaque switching rates.

Candida albicans is a normal member of the human microbiome and an opportunistic fungal pathogen. This species undergoes several morphological transitions, and here we consider white-opaque switching. In this switching program, C.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.

Background: Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context.

Evolution of the complex transcription network controlling biofilm formation in species.

We examine how a complex transcription network composed of seven 'master' regulators and hundreds of target genes evolved over a span of approximately 70 million years. The network controls biofilm formation in several species, a group of fungi that are present in humans both as constituents of the microbiota and as opportunistic pathogens. Using a variety of approaches, we observed two major types of changes that have occurred in the biofilm network since the four extant species we examined last shared a common ancestor.

Lineage-specific selection and the evolution of virulence in the clade.

is the most common cause of systemic fungal infections in humans and is considerably more virulent than its closest known relative, To investigate this difference, we constructed interspecies hybrids and quantified mRNA levels produced from each genome in the hybrid. This approach systematically identified expression differences in orthologous genes arising from -regulatory sequence changes that accumulated since the two species last shared a common ancestor, some 10 million y ago. We documented many orthologous gene-expression differences between the two species, and we pursued one striking observation: All 15 genes coding for the enzymes of glycolysis showed higher expression from the genome than the genome in the interspecies hybrid.

A Screen for Small Molecules to Target Biofilms.

The human fungal pathogen can form biofilms on biotic and abiotic surfaces, which are inherently resistant to antifungal drugs. We screened the Chembridge Small Molecule Diversity library containing 30,000 "drug-like" small molecules and identified 45 compounds that inhibited biofilm formation. These 45 compounds were then tested for their abilities to disrupt mature biofilms and for combinatorial interactions with fluconazole, amphotericin B, and caspofungin, the three antifungal drugs most commonly prescribed to treat infections.

An Opaque Cell-Specific Expression Program of Secreted Proteases and Transporters Allows Cell-Type Cooperation in .

An unusual feature of the opportunistic pathogen is its ability to switch stochastically between two distinct, heritable cell types called white and opaque. Here, we show that only opaque cells, in response to environmental signals, massively upregulate a specific group of secreted proteases and peptide transporters, allowing exceptionally efficient use of proteins as sources of nitrogen. We identify the specific proteases [members of the secreted aspartyl protease () family] needed for opaque cells to proliferate under these conditions, and we identify four transcriptional regulators of this specialized proteolysis and uptake program.

Combination of Antifungal Drugs and Protease Inhibitors Prevent Biofilm Formation and Disrupt Mature Biofilms.

Biofilms formed by the fungal pathogen are resistant to many of the antifungal agents commonly used in the clinic. Previous reports suggest that protease inhibitors, specifically inhibitors of aspartyl proteases, could be effective antibiofilm agents. We screened three protease inhibitor libraries, containing a total of 80 compounds for the abilities to prevent biofilm formation and to disrupt mature biofilms.

A Set of Diverse Genes Influence the Frequency of White-Opaque Switching in .

The fungal species is both a member of the human microbiome and a fungal pathogen. undergoes several different morphological transitions, including one called white-opaque switching. Here, cells reversibly switch between two states, "white" and "opaque," and each state is heritable through many cell generations.

A Selective Serotonin Reuptake Inhibitor, a Proton Pump Inhibitor, and Two Calcium Channel Blockers Inhibit Biofilms.

Biofilms formed by the human fungal pathogen are naturally resistant to many of the antifungal agents commonly used in the clinic. We screened a library containing 1600 clinically tested drug compounds to identify compounds that inhibit biofilm formation. The compounds that emerged from the initial screen were validated in a secondary screen and then tested for (1) their abilities to disrupt mature biofilms and (2) for synergistic interactions with representatives of the three antifungal agents most commonly prescribed to treat infections, fluconazole, amphotericin B, and caspofungin.

Corrigendum: Genetic Modification of Closely Related Candida Species.

[This corrects the article DOI: 10.3389/fmicb.2019.

Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit.

Changes in both the coding sequence of transcriptional regulators and in the cis-regulatory sequences recognized by these regulators have been implicated in the evolution of transcriptional circuits. However, little is known about how they evolved in concert. We describe an evolutionary pathway in fungi where a new transcriptional circuit (a-specific gene repression by the homeodomain protein Matα2) evolved by coding changes in this ancient regulator, followed millions of years later by cis-regulatory sequence changes in the genes of its future regulon.

A population shift between two heritable cell types of the pathogen is based both on switching and selective proliferation.

Differentiated cell types often retain their characteristics through many rounds of cell division. A simple example is found in , a member of the human microbiota and also the most prevalent fungal pathogen of humans; here, two distinct cell types (white and opaque) exist, and each one retains its specialized properties across many cell divisions. Switching between the two cell types is rare in standard laboratory medium (2% glucose) but can be increased by signals in the environment, for example, certain sugars.

Candida albicans white and opaque cells exhibit distinct spectra of organ colonization in mouse models of infection.

Candida albicans, a species of fungi, can thrive in diverse niches of its mammalian hosts; it is a normal resident of the GI tract and mucosal surfaces but it can also enter the bloodstream and colonize internal organs causing serious disease. The ability of C. albicans to thrive in these different host environments has been attributed, at least in part, to its ability to assume different morphological forms.

Genetic Modification of Closely Related Species.

Species from the genus are among the most important human fungal pathogens. Several of them are frequent commensals of the human microbiota but are also able to cause a variety of opportunistic infections, especially when the human host becomes immunocompromised. By far, most of the research to understand the molecular underpinnings of the pathogenesis of these species has focused on , the most virulent member of the genus.

Evaluation of SmearOFF, maleic acid and two EDTA preparations in smear layer removal from root canal dentin.

To evaluate SmearOFF, 7% maleic acid (MA) and two different preparations of ethylenediaminetetraacetic acid (EDTA) in smear layer removal. Fifty single-rooted teeth were separated into five groups, instrumented and irrigated as follows: (1) SmearOFF, (2) 7% MA, (3) 18% EDTA (pH 11.4), (4) 17% EDTA (pH 8.

Intrinsic cooperativity potentiates parallel -regulatory evolution.

Convergent evolutionary events in independent lineages provide an opportunity to understand why evolution favors certain outcomes over others. We studied such a case where a large set of genes-those coding for the ribosomal proteins-gained -regulatory sequences for a particular transcription regulator (Mcm1) in independent fungal lineages. We present evidence that these gains occurred because Mcm1 shares a mechanism of transcriptional activation with an ancestral regulator of the ribosomal protein genes, Rap1.

High Constitutive Activity Accounts for the Combination of Enhanced Direct Activation and Reduced Potentiation in Mutated GABA Receptors.

GABA receptors activated by the transmitter GABA are potentiated by several allosterically acting drugs, including the intravenous anesthetic propofol. Propofol can also directly activate the receptor, albeit at higher concentrations. Previous functional studies have identified amino acid residues whose substitution reduces potentiation of GABA-activated receptors by propofol while enhancing the ability of propofol to directly activate the receptor.