Evolution of a Fungal Gene Expression Regulator

Describing the largest analysis to date of the modified DNA base 5mC variations in fungi.

Parasitella parasitica (ZyGoLife Research Consortium on Flickr, CC BY-SA 2.0)

Parasitella parasitica, one of the fungi studied. (ZyGoLife Research Consortium on Flickr, CC BY-SA 2.0)

The Science

Changing an A, C, T or G in a genome sequence can lead to changes in protein structures and functions, but the DNA bases themselves can also be modified. The best-known example of a modified DNA base is a methylation of the base cytosine at the 5th position on its carbon ring, or 5mC. In many organisms, 5mC is an important piece of how they regulate their genomes, but is not well understood in fungi. A team of researchers reported on the largest analysis of 5mC distribution across the fungal tree of life to date, involving more than 500 species of fungi.

The Impact

Interactions between plants and fungi run the gamut from mutually beneficial to antagonistic. In fungi, 5mC is often found in transposable elements or transposons that can move to another location in the genome. Many plant pathogens such as the fungi that cause poplar leaf rust, are rich in transposons, which may help the pathogens evade a plant’s defenses. Understanding the role of transposons and 5mC in fungi could help researchers find ways to protect poplar and other crops being considered for bioenergy feedstock development.

Summary

With the aim of producing at least one reference genome for every family of fungi, the 1000 Fungal Genomes initiative of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, and others like it, are uncovering the true diversity of the fungal kingdom. The abundance of fungal genomes underscores the need for a more comprehensive exploration of genomic DNA modifications (epigenome).

Spinellus fusiger (ZyGoLife Research Consortium on Flickr, CC BY-SA 2.0)

Spinellus fusiger, one of the fungi studied. (ZyGoLife Research Consortium on Flickr, CC BY-SA 2.0)

In Nature Ecology & Evolution, a team led by Robert Schmitz at the University of Georgia and including JGI researchers conducted the largest analysis to date of 5mC, an important piece of the epigenome. Across the fungal tree of life, they tracked the evolution of 5mC pathways across 528 species.

The researchers found that unlike most flowering plants and animals, fungi lack gene body methylation. The analysis revealed that 5mC in some fungal species is abundant in repetitive DNA and transposons in methylated cytosine clusters (MCCs – similar to the MAC clusters for 6mA), rather than in genes, which suggests that 5mC may play a role in genome defense. Additionally, the team found a correlation between genome-wide 5mC abundance and the abundance of specific 5mC methyltransferase (MTase) variants.

Using new sequencing technologies for producing both reference genomes and epigenomics, researchers are unwrapping complex mechanisms of genome-wide regulation and cataloging them in JGI’s fungal portal MycoCosm.

Contacts:

BER Contact
Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
[email protected]

PI Contact
Robert Schmitz
University of Georgia, Athens
[email protected]

Funding:

The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The Georgia Advanced Computing Resource Center (GACRC) and Georgia Genomics and Bioinformatics Core (GGBC) at the University of Georgia provided sequencing and computational resources, respectively. This work was supported by the Office of the Vice President for Research at UGA.

Publication:

Bewick AJ et al. Diversity of cytosine methylation across the fungal tree of life. Nature Evol Evol. 2018 February 18. doi: 10.1038/s41559-019-0810-9.