About -rV ending verbs in the Sakhalin dialect of Ainu

Table S2. Abbreviations of peroxidase gene names used for the peroxidase-catalase superfamily. (XLSX 54 kb

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus <i>Exophiala dermatitidis</i> under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

<div><p><i>Exophiala dermatitidis (Wangiella dermatitidis</i>) belongs to the group of the so-called black yeasts. Thanks in part to its thick and strongly melanized cell walls, <i>E</i>. <i>dermatitidis</i> is extremely tolerant to various kinds of stress, including extreme pH, temperature and desiccation. <i>E</i>. <i>dermatitidis</i> is also the agent responsible for various severe illnesses in humans, such as pneumonia and keratitis, and might lead to fatal brain infections. Due to its association with the human environment, its poly-extremophilic lifestyle and its pathogenicity in humans, <i>E</i>. <i>dermatitidis</i> has become an important model organism. In this study we present the functional analysis of the transcriptional response of the fungus at 1°C and 45°C, in comparison with that at 37°C, for two different exposition times, i.e. 1 hour and 1 week. At 1°C, <i>E</i>. <i>dermatitidis</i> uses a large repertoire of tools to acclimatize, such as lipid membrane fluidization, trehalose production or cytoskeleton rearrangement, which allows the fungus to remain metabolically active. At 45°C, the fungus drifts into a replicative state and increases the activity of the Golgi apparatus. As a novel finding, our study provides evidence that, apart from the protein coding genes, non-coding RNAs, circular RNAs as well as fusion-transcripts are differentially regulated and that the function of the fusion-transcripts can be related to the corresponding temperature condition. This work establishes that <i>E</i>. <i>dermatitidis</i> adapts to its environment by modulating coding and non-coding gene transcription levels and through the regulation of chimeric and circular RNAs.</p></div

Image_1_Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?.JPEG

<p>The black yeast Exophiala dermatitidis is a polyextremophilic human pathogen, especially known for growing in man-made extreme environments. Reported diseases caused by this fungus range from benign cutaneous to systemic infections with 40% fatality rate. While the number of cases steadily increases in both immunocompromised and immunocompetent people, detailed knowledge about infection mechanisms, virulence factors and host response are scarce. To understand the impact of the putative virulence factor melanin on the infection, we generated a polyketide synthase (PKS1) mutant using CRISPR/Cas9 resulting in a melanin deficient strain. The mutant and the wild-type fungus were inoculated onto skin explants using an ex vivo skin organ culture model to simulate in vivo cutaneous infection. The difference between the mutant and wild-type transcriptional landscapes, as assessed by whole RNA-sequencing, were small and were observed in pathways related to the copper homeostasis, cell wall genes and proteases. Seven days after inoculation the wild-type fungus completely colonized the stratum corneum, invaded the skin and infected keratinocytes while the mutant had only partially covered the skin and showed no invasiveness. Our results suggest that melanin dramatically improves the invasiveness and virulence of E. dermatitidis during the first days of the skin infection.</p

Pie chart of the summarized Gene Ontology (GO) terms for different conditions.

<p>(A) Over-represented BP-related GO terms for the genes upregulated at 1°C for 1 hour. (B) Over-represented GO terms related to biological processes (BP) for the genes up-regulated at 1°C for 1 week. (C) Over-represented BP-related GO terms for the genes down-regulated at 1°C for 1 week. (D) Over-represented CC-related GO terms for the genes up-regulated at 1°C for 1 week. (E) Over-represented BP-related GO terms for the genes down-regulated at 45°C for 1hour. (F) Over-represented BP-related GO terms for the genes up-regulated at 45°C for 1 week. (G) Over-represented BP-related GO terms for the genes down-regulated at 45°C for 1 week. (H) Over-represented BP-related GO terms for the genes up-regulated at both 45C1H and 45C1W.</p

Graphical representation of the chimeric RNAs with the highest number of split reads for different temperatures.

<p>Fusion transcripts present at the following experimental conditions: 1°C for 1 week (A), 37°C (B) and 45°C for 1 week (C). The thick blue arrow represents the Supercontig with the corresponding scale. The start codon is represented by the green arrow. The stop codon is shown as a red vertical line. The splice connecting both genes is shown in black and the number of supporting split reads is located between both fused genes. The blue regions represent the Coding DNA Sequence (CDS), the dark grey regions represent the Untranslated Regions (UTRs), while the light gray regions represent introns. The splicing direction is given by the black arrow head.</p

Table_1_Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?.XLS

<p>The black yeast Exophiala dermatitidis is a polyextremophilic human pathogen, especially known for growing in man-made extreme environments. Reported diseases caused by this fungus range from benign cutaneous to systemic infections with 40% fatality rate. While the number of cases steadily increases in both immunocompromised and immunocompetent people, detailed knowledge about infection mechanisms, virulence factors and host response are scarce. To understand the impact of the putative virulence factor melanin on the infection, we generated a polyketide synthase (PKS1) mutant using CRISPR/Cas9 resulting in a melanin deficient strain. The mutant and the wild-type fungus were inoculated onto skin explants using an ex vivo skin organ culture model to simulate in vivo cutaneous infection. The difference between the mutant and wild-type transcriptional landscapes, as assessed by whole RNA-sequencing, were small and were observed in pathways related to the copper homeostasis, cell wall genes and proteases. Seven days after inoculation the wild-type fungus completely colonized the stratum corneum, invaded the skin and infected keratinocytes while the mutant had only partially covered the skin and showed no invasiveness. Our results suggest that melanin dramatically improves the invasiveness and virulence of E. dermatitidis during the first days of the skin infection.</p

Representation of up- and down-regulated genes for cold and hot conditions, compared to 37°C.

<p>Upwards and downwards arrows represent up- and down-regulated genes, respectively. Protein coding genes (A) show the highest number of differentially expressed genes following the treatment at 1°C for 1 week (1C1W), with a total of 609 and 288 down- and up-regulated genes, respectively. NcRNA genes (B) show the highest number of differentially expressed genes at the same experimental condition (1°C for 1 week, 1C1W), with a total of 30 and 6 up- and downregulated genes, respectively. For both coding and non-coding genes, the smallest number of differentially expressed genes is found when the fungus have been exposed at 45°C for 1 week (45C1W).</p