Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar

Principal-component analysis of 7,942 genes differentially expressed across all time points (n = 3 for each time point; T = 0, 1, 2, 3, 4, 5, 6, 12, 16, or 24 h postgermination). Each time point is color coded.

Resting-spore-specific expression. (Top) Heat map displaying the absence (blue) or presence (red) of 10 or more transcripts for a given gene over time. The average percentage of the transcriptome expressed at any given time point is given below. (Bottom) Coexpression diagram, where each node represents a gene only expressed in ungerminated spores. Nodes linked to 10 or more others are highlighted in yellow, with their functions shown adjacent.

Clustering of expression over time. (A) Heat map displaying differentially expressed genes. Expression levels are plotted in log₂, space and mean centered (FDR of <0.001) across the entire time course. k-means clustering has partitioned genes into 7 clusters, as indicated by colored bars and numbered graphs below the heat map. (B) Graphs displaying cluster expression over time (0 to 24 h). (C) Table displaying categories enriched (hypergeometric test, corrected P value of <0.05), indicated in red, for clusters 1 to 7.

Differential gene expression over time. (A) The number of genes significantly differentially expressed (multiply corrected P value of <0.05) between time points, shown over time. Green bars indicate genes with an increase in expression (log fold change [FC] of >2), while red bars indicate genes with a decrease in expression (log FC of <−2). (B) Enriched categories for the up- or downregulated genes over time. Green boxes indicate an overall upregulation of this category, red indicates an overall downregulation and red-green hatching indicates mixed regulation of this category. (C) Expression profiles of transcripts in specific categories over time, with the number of transcripts represented by each trend shown in parentheses.

Cell wall dynamics and inhibition of germination. (A) Spores germinated for 0, 3, 6, 12, and 24 h, stained with calcofluor white (CFW), fluorescein (FITC), and ROS stain carboxy-H₂DCFDA (ROS). (B) Germination is inhibited by 5 mM hydrogen peroxide and over 1.5 nM antimycin A, as determined by live-cell imaging, after 5 h of germination in SAB. The hydrogen peroxide control consists of an equivalent volume of H₂O, and the antimycin A control consists of an equivalent volume of 100% ethanol.