Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae

Abstract

BackgroundThe rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. oryzae a compelling target for sRNA profiling. We have examined sRNA species and their biosynthetic genes in M. oryzae, and the degree to which these elements regulate fungal stress responses. To this end, we have characterized sRNAs under different physiological stress conditions, which had not yet been examined in this fungus.ResultsThe resulting libraries are composed of more than 37 million total genome matched reads mapping to intergenic regions, coding sequences, retrotransposons, inverted, tandem, and other repeated regions of the genome with more than half of the small RNAs arising from intergenic regions. The 24 nucleotide (nt) size class of sRNAs was predominant. A comparison to transcriptional data of M. oryzae undergoing the same physiological stresses indicates that sRNAs play a role in transcriptional regulation for a small subset of genes. Support for this idea comes from generation and characterization of mutants putatively involved in sRNAs biogenesis; our results indicate that the deletion of Dicer-like genes and an RNA-Dependent RNA Polymerase gene increases the transcriptional regulation of this subset of genes, including one involved in virulence.ConclusionsVarious physiological stressors and in planta conditions alter the small RNA profile of the rice blast fungus. Characterization of sRNA biosynthetic mutants helps to clarify the role of sRNAs in transcriptional control.

A fungal Argonaute interferes with RNA interference

“…In our previous RNA-seq analysis, very few TEs were transcriptionally active (23). This was also indicated in this study, as the portion of TE-derived sRNAs was extremely low compared to that previously reported in rice-infecting P. oryzae strains (Table 1; (28,52)). Considering recent findings on the contributions of TEs to the genome plasticity and evolution in fungi, MoAGO2 might become a very unique modulator for maintaining TEs moderately active to generate new genetic variations in this phytopathogenic fungus.…”

Conversations between kingdoms: small RNAs

“…However, some pathogen-produced sRNAs are capable of inducing gene silencing in the plants, too. A positive role of sRNAs in fungal virulence is supported by the fact that fungal sRNAs differentially accumulate during the infection process [56,57]. Moreover, the aggressive fungal plant pathogen Botrytis cinerea produces sRNAs (Bc-sRNAs) that move into the host plant cell during early infection and hijack the host AGO, the key protein in the RNAi machinery, to silence important host immunity genes [56].…”

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

“…Small RNAs have been studied in several pathosystems [25], [26], [27], [28], [29], but their role in regulating pathogen biology and host-pathogen interactions is poorly understood. Endogenous silencing pathways and differential expression of different classes of small RNAs during host-pathogen interaction remain to be characterized for most pathogens, including Phytophthora species.…”