Extracellular Vesicle-Mediated RNA Release in Histoplasma capsulatum

Abstract

Eukaryotic cells, including fungi, release extracellular vesicles (EVs). These lipid bilayered compartments play essential roles in cellular communication and pathogenesis. EV composition is complex and includes proteins, glycans, pigments, and RNA. RNAs with putative roles in pathogenesis have been described in EVs produced by fungi. Here we describe the RNA content in EVs produced by the G186AR and G217B strains of Histoplasma capsulatum, an important human-pathogenic fungal pathogen. A total of 124 mRNAs were identified in both strains. In this set of RNA classes, 93 transcripts were enriched in EVs from the G217B strain, whereas 31 were enriched in EVs produced by the G186AR strain. This result suggests that there are important strain-specific properties in the mRNA composition of fungal EVs. We also identified short fragments (25 to 40 nucleotides in length) that were strain specific, with a greater number identified in EVs produced by the G217B strain. Remarkably, the most highly enriched processes were stress responses and translation. Half of these fragments aligned to the reverse strand of the transcript, suggesting the occurrence of microRNA (miRNA)-like molecules in fungal EVs. We also compared the transcriptome profiles of H. capsulatum with the RNA composition of EVs, and no correlation was observed. Taking the results together, our study provided information about the RNA molecules present in H. capsulatum EVs and about the differences in composition between the strains. In addition, we found no correlation between the most highly expressed transcripts in the cell and their presence in the EVs, reinforcing the idea that the RNAs were directed to the EVs by a regulated mechanism.IMPORTANCE Extracellular vesicles (EVs) play important roles in cellular communication and pathogenesis. The RNA molecules in EVs have been implicated in a variety of processes. EV-associated RNA classes have recently been described in pathogenic fungi; however, only a few reports of studies describing the RNAs in fungal EVs are available. Improved knowledge of EV-associated RNA will contribute to the understanding of their role during infection. In this study, we described the RNA content in EVs produced by two isolates of Histoplasma capsulatum Our results add this important pathogen to the current short list of fungal species with the ability to use EVs for the extracellular release of RNA.

Keywords: Histoplasma capsulatum; RNA; extracellular vesicles.

FIG 1

Gene ontology analysis. The pie charts present the gene ontology of mRNA sequences enriched in EVs isolated from (A) H. capsulatum G217B (n = 93) and (B) H. capsulatum G186AR (n = 31).

FIG 2

RNA secondary structure. We used ppFold software to predict the secondary structure from the putative miRNAs extracted from the obtained reads. The numbers in parentheses represent the alignment E values. The colors indicated for the nucleotides represent the reliability percentage for each position of the RNA molecule (bottom panel). The stability value corresponding to each structure is given in kilocalories/mole.

FIG 3

Gene ontology analysis. The pie charts present the gene ontology of mRNA sequences enriched in H. capsulatum cells (A) and in EVs isolated from H. capsulatum (B).