The bdelloid rotifer Adineta vaga under a polychromatic polarization microscope
a microscope image of a rotifer

Bacterial Enzyme Keeps Rotifers’ Transposable Elements in Check

Jumping genes in bdelloid rotifers are tamped down by DNA methylation performed by an enzyme pilfered from bacteria roughly 60 million years ago, a study finds.

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Christie Wilcox

Christie joined The Scientist's team as Newsletter Editor in 2021, after more than a decade of science writing. She has a PhD in cell and molecular biology, and her debut book Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry, received widespread acclaim.

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Mar 3, 2022

ABOVE: The bdelloid rotifer Adineta vaga under a polychromatic polarization microscope Courtesy of Michael Shribak, Irina Yushenova

Bdelloid rotifers, microscopic animals found nearly all in freshwater ecosystems worldwide, lack the enzymes that most animals use to silence regions of their genome by attaching chemical tags called methyl groups. Instead, their methyl silencing system employs a bacterial enzyme that made its way into the animals around 60 million years ago, researchers reported Monday (February 28) in Nature Communications.

Emmelien Vancaester, a bioinformatician at the Wellcome Sanger Institute in the UK who was not involved in the study, says she finds the study “quite convincing.”

“I think it’s really clear that this is a functional [epigenetic system] . . . a novel way of regulation in rotifers that has not been seen in metazoans before,” she says, noting that the system’s novelty supports the hypothesis that the gene encoding the enzyme originated in a bacterium and was integrated into the rotifer genome. “That a horizontally transferred gene has the ability to influence the transcription of a genome . . . I think that’s quite novel.”

The enzyme has completely reshaped the rotifers’ epigenetic system, says study coauthor Irina Arkhipova, a molecular evolutionary geneticist with the Marine Biological Laboratory in Woods Hole, Massachusetts. Currently, little is known about the epigenetic systems in rotifers, says Jae-Seong Lee, a rotifer molecular biologist at Sungkyunkwan University in South Korea who was not involved in the new study—despite the animals’ ecological importance. “Rotifers fill important ecological roles in many inland waters, both fresh and saline. Therefore, it is very important to understand their evolutionary adaptation mechanisms,” Lee writes in an email to The Scientist.

In addition to providing insights into rotifers, the enzyme “provides a glimpse,” says Arkhipova, “into the sequence of events that had to occur in early evolution of plants and animals,” when eukaryotic gene regulation systems initially evolved.

Reprogramming epigenetics

Shortly after eukaryotes evolved, they obtained enzymes from bacteria called C5-methyltransferases that attach methyl groups to cytosine residues in nucleic acids, effectively regulating gene expression. Among other things, this regulation allows cells within the body to take on different roles and keeps transposable elements (TEs) from excessively jumping around and wreaking genomic havoc—in most animals, anyway. Bdelloid rotifers lack the methyltransferases of many of their metazoan kin.  

Arkhipova and her colleagues didn’t set out to find such a methyltransferase, but they happened upon it while sifting through the animals’ impressive repertoire of genes they’ve acquired from other organisms. “Bdelloids are currently the record holders in the amount of horizontally transferred genes,” she explains. As she and her colleagues initially reported in 2008, up to 10 percent of the animals’ genomes comes from other species, including plants, fungi, and bacteria—at least an order of magnitude more than seen in other animals.

They are an evolutionary scandal.

—Chiara Boschetti, University of Plymouth, echoing John Maynard Smith

While annotating these stolen genes in the bdelloid Adineta vaga, the team flagged one “because it was a methyltransferase,” Arkhipova says—one relatively new to Adineta vaga’s genome. DNA methyltransferases in eukaryotes are thought to have evolved near the origin of the group, before plants, fungi, and animals split from one another. The enzyme Arkhipova’s group found seemed to be one that had been thought to be exclusive to bacteria, a so-called N4C-methyltransferase that adds methyl groups to a different part of cytosine bases than the methyltransferases in other animals. Indeed, the enzyme “was most similar to bacterial restriction modification enzymes, which bacteria used to defend themselves from phage infections, but in this case, it was not associated with any type of restriction modification system,” Arkhipova explains.

Genomic comparisons soon revealed that the enzyme was present in representatives from each of the major families in the class Bdelloidea, so the team decided to investigate what it might be doing in the animals. One clue was that the putative bacterial enzyme was attached to a eukaryotic motif common to chromatin-binding proteins that attaches to certain methylated histones. Scanning the rotifer genome for the kind of methylation marks known to be made by this enzyme in bacteria, team member Fernando Rodriguez, who is in Arkhipova’s lab, discovered the animals do indeed have these epigenetic marks, and they are largely concentrated on transposable element sequences, as well as some tandem repeats.

Biochemist and collaborator Irina Yushenova then took the gene for the enzyme and expressed it in E. coli, demonstrating that it does, in fact, generate 4mC marks that could be detected using specific antibodies. Yushenova further demonstrated that bdelloids possess a histone methyltransferase that preferentially recognizes 4mC marks on DNA, using them to steer its methylation of histones. The two methyltransferases therefore likely work in tandem to reinforce gene silencing, the team concludes, with histone methylation prompting DNA methylation and vice versa.

In many ways, it’s similar to the methylation system used by other animals, but it’s a much more recent acquisition, says Arkhipova. The bacteria-derived methyltransferase was in all bdelloids examined but missing from the genomes of rotifers from the class Monogononta, suggesting the transfer occurred after bdelloids split into their own group about 60 million years ago. In contrast, the methyltransferase systems in other animals are thought to have evolved repeatedly before the major split between eukaryotic kingdoms more than a billion years ago. The rotifers’ enzyme acquisition is “kind of a recapitulation of this process that occurred very early in evolution, but with a different enzyme,” she says.

Adding to bdelloids’ collection of quirks

Bdelloid rotifers were already considered biological oddities. In addition to their high percentage of DNA pilfered from other organisms, they appear to have shirked sexual reproduction for the better part of 60 million years, making them a curious case study for understanding the purpose of sex. In short, “they are an evolutionary scandal,” says Chiara Boschetti, an evolutionary molecular biologist at University of Plymouth in the UK who studies rotifers, echoing the words of evolutionary biologist John Maynard Smith.

The repurposed bacterial enzyme may help explain how the animals are able to persist as predominately asexual organisms. Arkhipova notes that rotifers “cannot take advantage of frequent sexual recombination as the means to get rid of deleterious transposable element insertions.” Yet these TEs, also known as jumping genes, only account for a few percent of the microscopic animals’ genomes, far less than in many other animals. The fact that the 4mC marks were concentrated on TEs led her to postulate that the enzyme “may have been an adaptation to help them to keep their transposable elements in check.” In light of rotifers’ strangeness, the new study’s proposition that the animals’ epigenetic system is unique among metazoans may not be that surprising. However, the study helps confirm aspects of the animals’ biology that have been somewhat contested—such as the volume of horizontally transferred genes—and it does so robustly, with multiple reinforcing experiments, Boschetti says.

“They’ve really proved in this paper that this alternative way of methylation occurs in rotifers,” Vancaester says.

Lee says he found the paper especially fascinating because epigenetic mechanisms can contribute to adaptation and plasticity in asexual species, increasing their capacity to respond to rapid environmental changes than alterations to the genome itself could. He and his colleagues have suggested, for example, that histone methylation in the non-bdelloid, asexual rotifer Brachionus koreanus may help the species adapt to ocean acidification.

Arkhipova says she and her team are also intrigued by the methylation marks on tandem repeats and are interested in uncovering their purpose. And they would like to study potentially unusual functions of other foreign genes detected in rotifers, she says.

Vancaester says it’s an exciting time to study horizontal gene transfer (HGT). This and many other papers show that HGT in eukaryotes not only happens, but “can have an effect on evolution,” she notes. “I just think it fits in a whole bubble of papers right now that shows that HGT is relevant.”

Clarification (March 4): The text has been updated to note the original source of the term “evolutionary scandal.”