Cross-species transcriptomics identifies core regulatory changes differentiating the asymptomatic asexual and virulent sexual life cycles of grass-symbiotic Epichloë fungi

Abstract

Fungi from the genus Epichloë form systemic endobiotic infections of cool season grasses, producing a range of host-protective natural products in return for access to nutrients. These infections are asymptomatic during vegetative host growth, with associations between asexual Epichloë spp. and their hosts considered mutualistic. However, the sexual cycle of Epichloë spp. involves virulent growth, characterized by the envelopment and sterilization of a developing host inflorescence by a dense sheath of mycelia known as a stroma. Microscopic analysis of stromata revealed a dramatic increase in hyphal propagation and host degradation compared to asymptomatic tissues. RNAseq was used to identify differentially expressed genes (DEGs) in asymptomatic vs. stromatized tissues from three diverse Epichloë–host associations. Comparative analysis identified a core set of 135 DEGs that exhibited conserved transcriptional changes across all three associations. The core DEGs more strongly expressed during virulent growth encode proteins associated with host suppression, digestion, adaptation to the external environment, a biosynthetic gene cluster (BGC), and five transcription factors that may regulate Epichloë stroma formation. An additional five transcription factor encoding DEGs were suppressed during virulent growth, suggesting they regulate mutualistic processes. Expression of BGCs for natural products that suppress herbivory was universally suppressed during virulent growth, and additional BGCs that may encode production of novel host-protective natural products were identified. A comparative analysis of 26 Epichloë genomes found a general decrease in core DEG conservation among asexual species, and a specific decrease in conservation for the BGC expressed during virulent growth and an unusual uncharacterized gene.

Dissection of the epoxyjanthitrem pathway in Epichloë sp. LpTG-3 strain AR37 by CRISPR gene editing

“…Samples were analysed according to Berry et al (2022). For the epoxyjanthitrems, due to the instability of epoxyjanthitrems as pure compounds, the peak areas and known concentrations of the reference samples (AR37) were used to determine response factors, which were used to subsequently quantify each epoxyjanthitrem compound in the samples.…”

Two Iron(II), α-Ketoglutarate-Dependent Enzymes Encoded by the PPZ Gene Cluster of Metarhizium majus Enable Production of 8-Hydroxyperamine

“…use an alternative source of hydroxyproline for peramine biosynthesis. One notable exception was the Epichloë typhina strain E8, known to be a particularly strong producer of peramine . This strain contains the gene Ety8_004252 which encodes a protein that shares 61% sequence homology with PpzD.…”

“…One notable exception was the Epichloëtyphina strain E8, known to be a particularly strong producer of peramine. 26 This strain contains the gene Ety8_004252 which encodes a protein that shares 61% sequence homology with PpzD. Like ppzA from E. typhina E8, the pattern of gene regulation of Ety8_004252 suggests that it is involved in symbiosis between E. typhina E8 and its host.…”

“…Like ppzA from E. typhina E8, the pattern of gene regulation of Ety8_004252 suggests that it is involved in symbiosis between E. typhina E8 and its host. 26 However, Ety8_004252 also forms part of a larger gene cluster that does not include ppzA, 26 so more research is required to determine if it plays a role in peramine biosynthesis. Regardless, introducing ppzD into other peramine-producing Epichloëspp.…”

“…This strain contains the gene Ety8_004252 which encodes a protein that shares 61% sequence homology with PpzD. Like ppzA from E. typhina E8, the pattern of gene regulation of Ety8_004252 suggests that it is involved in symbiosis between E. typhina E8 and its host . However, Ety8_004252 also forms part of a larger gene cluster that does not include ppzA , so more research is required to determine if it plays a role in peramine biosynthesis.…”