Discovering the hidden function in fungal genomes

Abstract

New molecular technologies have helped unveil previously unexplored facets of the genome beyond the canonical proteome, including microproteins and short ORFs, products of alternative splicing, regulatory non-coding RNAs, as well as transposable elements, cis-regulatory DNA, and other highly repetitive regions of DNA. In this Review, we highlight what is known about this 'hidden genome' within the fungal kingdom. Using well-established model systems as a contextual framework, we describe key elements of this hidden genome in diverse fungal species, and explore how these factors perform critical functions in regulating fungal metabolism, stress tolerance, and pathogenesis. Finally, we discuss new technologies that may be adapted to further characterize the hidden genome in fungi.

Fig. 1. Functional products of DNA expression, including components of the hidden genome.

Sources of function from DNA include: production of mRNA and the resulting canonical proteins that are the focus of most genomic research; alternatively spliced RNA and protein products, including introns that are capable of becoming fixed in a cell and regulating gene expression; ubiquitous transcription of diverse non-coding RNAs that play important roles via their interaction with DNA, RNA, and proteins; the expression of pseudogenized DNA and dubious ORFs into functional proteins; the existence of non-coding regulatory elements (NCREs) that regulate gene expression; transposable elements that may move within the genome or between cells within or outside of the originating species, along with other repetitive DNA that may facilitate structural rearrangements in the genome. Figure 1, created with BioRender.com, released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.

Fig. 2. The nature of lncRNA transcription and examples of intergenic lncRNAs in fungi.

LncRNAs exist in several different orientations relative to canonical ORFs within fungal genomes, including in between exons (intronic), in between genes (intergenic), as well as within genes in either the same (sense) or opposite (antisense) direction as the larger ORF. Many lncRNAs have been characterized in diverse fungal species, including: the lncRNA DINOR in Candida auris that affects fungal morphology and drug resistance; the putatively cis-acting lncRNA sequence RZE1 in Cryptococcus neoformans that recapitulates virulence phenotypes of the neighboring gene ZNF2 when deleted and appears to affect the proportion of mRNA of ZNF2 that is localized to the nucleus; and the lncRNA nc-tgp1 that alters sensitivity to environmental stressors in Schizosaccharomyces pombe by increasing nucleosome occupancy when actively transcribed, excluding the transcription factor Pho7 from binding and activating expression of the downstream tgp1 gene. Figure 2, created with BioRender.com, released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.

Fig. 3. The movement of transposable elements (TEs) within and between fungal genomes.

In the human fungal pathogen Cryptococcus deneoformans, the mobility of several different TEs is stress-responsive, including during infection and at the elevated (host-relevant) temperature of 37 °C. Insertion of mobilized TEs in this pathogen also appears to be biased depending on the type of TE, and has been associated with a decrease in susceptibility to antifungal drugs. The accumulation of the Cnl1 TE at subtelomeric regions, for example, can result in additional copies of Cnl1 being driven towards other sites in the genome, which may influence drug response and virulence phenotypes. The rate of other genomic changes, including from single nucleotide polymorphisms (SNPs) and insertion/deletion (indel) mutations, remain unchanged at elevated temperatures, suggesting TE mobility is a primary driver of genomic change during heat stress. In the plant fungal pathogen Pyrenophora tritici-repentis, the toxhAT TE contains the ToxA gene which can induce cell death in susceptible wheat strains during infection. The toxhAT TE has been observed to move between isolates of the same species, as well as between different species entirely. While toxhAT has been observed to exist within larger Starship TEs, there is also evidence to suggest that it is able to mobilize from the genome independently. Figure 3, created with BioRender.com, released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.