A black truffle
Black truffles, also known as Périgord truffles, grow in symbiosis with the roots of oak and hazelnut trees. In the world of haute cuisine, they are expensive and highly prized.
In the world of epigenetics, however, the fungi (Tuber melanosporum) are of major interest for another reason: their unique pattern of DNA methylation, a biochemical process that chemically modifies nucleic acids without changing their sequence. Epigenetics is the study of changes in gene expression caused by mechanisms other than changes in the DNA sequence.
A newly published study in the journal Genome Biology by scientists from UCLA and colleagues in Italy, France and Taiwan reports on the truffle’s unique genetic makeup.
“The fungi have a complex genome, with a preponderance of repetitive and mobile elements,” said Simone Ottonello of the laboratory of functional genomics and protein engineering at the University of Parma in Italy. “The genome resembles the composition of the human genome, which also uses reversible methylation — and other mechanisms — to deal with repeated and mobile elements.”
More than 58 percent of Tuber melanosporum’s genetic material is made up of so-called “jumping genes,” transposable genetic elements, or transposons, that can replicate and paste themselves throughout the genome. The research illustrates how the truffle regulates those elements.
“We found that DNA methylation is targeted to those transposable elements, but it also can affect the expression of adjacent genes and the number of transposons that are copied,” said Matteo Pellegrini, a professor of molecular, cell and developmental biology in the UCLA College, and the paper’s senior author.
The black truffle uses reversible epigenetic processes to regulate its genes and adapt to changes in its surroundings. Although this process was known to occur in other plants and animals, this was the first research to establish that it occurs in fungi.
Pellegrini said the new findings could shed light on how the reversible methylation helps the truffle adapt to its surroundings. “Because the truffle lives underground and doesn’t have an active spore dispersal system, it might need this plasticity to adapt to sudden environmental changes.”
The study’s lead author was Barbara Montanini, a research associate in Ottonello’s laboratory. Co-authors included Pao-Yang Chen, a UCLA assistant researcher in molecular, cell and developmental biology, and scientists from Taiwan’s Academia Sinica and the French National Institute for Agricultural Research (INRA).
The research was funded by the UCLA-DOE Institute for Genomics and Proteomics, the Fondazione Cariparma and Italy’s Ministry of Education, University and Research.
The article is available for free under the journal’s open access policy.