Epigenetic Control of Phenotypic Plasticity in the Filamentous Fungus Neurospora crassa

Abstract

Phenotypic plasticity is the ability of a genotype to produce different phenotypes under different environmental or developmental conditions. Phenotypic plasticity is a ubiquitous feature of living organisms, and is typically based on variable patterns of gene expression. However, the mechanisms by which gene expression is influenced and regulated during plastic responses are poorly understood in most organisms. While modifications to DNA and histone proteins have been implicated as likely candidates for generating and regulating phenotypic plasticity, specific details of each modification and its mode of operation have remained largely unknown. In this study, we investigated how epigenetic mechanisms affect phenotypic plasticity in the filamentous fungus Neurospora crassa. By measuring reaction norms of strains that are deficient in one of several key physiological processes, we show that epigenetic mechanisms play a role in homeostasis and phenotypic plasticity of the fungus across a range of controlled environments. In general, effects on plasticity are specific to an environment and mechanism, indicating that epigenetic regulation is context dependent and is not governed by general plasticity genes. Specifically, we found that, in Neurospora, histone methylation at H3K36 affected plastic response to high temperatures, H3K4 methylation affected plastic response to pH, but H3K27 methylation had no effect. Similarly, DNA methylation had only a small effect in response to sucrose. Histone deacetylation mainly decreased reaction norm elevation, as did genes involved in histone demethylation and acetylation. In contrast, the RNA interference pathway was involved in plastic responses to multiple environments.

New Insight Into Pathogenicity and Secondary Metabolism of the Plant Pathogen Penicillium expansum Through Deletion of the Epigenetic Reader SntB

“…Several previous reports described the role of epigenetics in the regulation of phenotypic alterations in filamentous fungi. Epigenetic mechanisms, e.g., histone modifications and RNA interference pathway, were found to be involved in phenotypic plasticity (i.e., phenotypic changes in the colony morphology) of N. crassa across an array of controlled environments including temperature, pH, osmotic stress and sugar content (Kronholm et al, 2016). Comparable results were previously gathered in the dimorphic yeast Aureobasidium pullulans, where phenotypic switches from yeast to mycelial form are likely to be an epigenetic phenomenon (Slepecky and Starmer, 2009).…”

“…In A. flavus, the deletion of sntB has led to various morphological phenotypes, such as reduced radial growth and reduced sclerotia formation (Pfannenstiel et al, 2018). Along the same line, snt2 deletion mutants of Fusarium oxysporum and Neurospora crassa, displayed morphological aberrations, including a drop in conidia formation and biomass accumulation, delayed vegetative growth and recurrent hyphal septation (Denisov et al, 2011;Kronholm et al, 2016). Although there have been several studies involved with SntB in ascomycetes, further data are needed to establish a congruent storyline about the impact of SntB on fungal development.…”

Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans

“…The underlining explanation of the division into frequent sexual reproduction of P. infestans strains, as found in Northern Europe versus the clonal lineages in Western Europe, appears to be regulated by complex events. Epigenetic influences during sexual reproduction, such as DNA methylation, histone modification and small RNAs (sRNAs), have been reported in several organisms including plants, animals and fungi (Quadrana and Colot, 2016;Kronholm et al, 2016;Donkin and Barrès, 2018). So far, no evidence of 5-methylcytosine DNA-methylation, which is prevalent in many organisms, has been reported in P. infestans (van West et al, 2008).…”

“…It is known that ploidy levels in P. infestans strains can vary (Goss et al, 2014;Knaus et al, 2016). Here we inferred the ploidy status of the P. infestans strains by exploiting the distribution of read counts at biallelic SNPs.…”

Chromatin Structure and Drug Resistance in Candida spp.

“…The genetic architecture of phenotypic plasticity is not fully known. However, the majority of evidence to date suggests that epigenetic and not genetic mechanisms dictate phenotypic plasticity in pathogenic microbes [ 73 , 74 ]. Epigenetics is defined as the inheritance of a phenotypic state that is not dependent on DNA sequence [ 75 ].…”