The PAC-3 transcription factor critically regulates phenotype-associated genes in Neurospora crassa

Abstract

Transcription factors play an important role in fungal environmental adaptive process by promoting adjustment to challenging stimuli via gene modulation and activation of signaling networks. The transcription factor encoded by the pac-3/rim101/pacC gene is involved in pH regulation and is associated with a wide variety of cellular functions. The deletion of pac-3 affects fungal development. In Neurospora crassa, the Δpac-3 strain presents diminished aerial growth and reduced conidiation. However, the PAC-3-regulated genes associated with this altered phenotype have not been elucidated. In this study, we used RNA-seq to analyze the phenotypic plasticity induced after pac-3 deletion in the filamentous fungus N. crassa cultivated in media supplemented with sufficient or limited inorganic phosphate. Genes related to morphology, hyphal development, and conidiation were of particular interest in this study. Our results suggest a pac-3 dependency in gene regulation in a Pi-dependent manner. Furthermore, our analysis suggested that the fungus attempts to overcome the deletion effects in a Δpac-3 mutant through a complex combined regulatory mechanism. Finally, the modulatory responses observed in the Δpac-3 strain, a double mutant generated based on the Δmus-52 mutant strain, is strain-specific, highlighting that the phenotypic impact may be attributed to pac-3 absence despite the combined mus-52 deletion.

Figure 1. Heatmap of morphology and development regulation-associated genes from N. crassa mutants. The hierarchical clustering of expression patterns for the 55 differentially expressed genes identified in the Δpac-3Δmus-52 mutant strain versus Δmus-52 is compared to the modulatory pattern observed for the same genes in the Δmus-52, evaluated in comparison to the wild-type strain. Expression levels were loaded into the MultiExperiment Viewer (MeV) and analyzed using average-linkage hierarchical clustering with a Pearson correlation coefficient distance metric. The intensity of color represents the value of upregulation (red) or downregulation (green) in log2FC.