Adapting with a Little Help from Jumping Genes

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The tale of the peppered moth (Biston betularia) is, quite literally, a textbook story of adaptive evolution. Back in the early 19th century, only one form of these now-iconic moths was known: a light variety speckled with dark spots (hence the name). In 1864, though, a naturalist in England first documented an all-dark moth—what seemed at the time to be little more than a curious example of melanin overproduction. Then came the Industrial Revolution, and dark moths took over, their inky wings reducing the odds of the nocturnal insects being eaten while they rested on soot-stained trees during the day. More than a century later, scientists discovered that the genetic tweak underscoring the moths’ dark pigmentation was a transposable element (TE).

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About 200 years ago, researchers estimate, nearly 22,000 nucleotides leapt into the first intron of a moth gene called cortex, and in doing so, dramatically increased the production of the protein it codes for—a key player in wing development and coloration.

TEs, also called transposons or jumping genes, are often cast in a negative evolutionary light. And there is a reason for that: when these sequences insert themselves into new places in the genome, they can mess up genes or alter their expression. They’re sometimes called junk DNA, or worse, genomic parasites, the idea being that they would mutate their host genomes into oblivion if they weren’t almost always silenced by epigenetic modifications such as methylation. But recent research is illuminating the intricacies of TE function and adding texture to this simplistic model.

“I don’t see them as parasites,” says Marie Mirouze, a plant genomicist at the French National Research Institute for Sustainable Development (IRD) in Marseille. “I rather see them as living in symbiosis with the host.” Indeed, some TEs become so embedded in their hosts’ biology that they are considered “domesticated,” losing the ability to jump around. For some time now, researchers have uncovered various ways in which that symbiosis has benefited organisms, from the development of placentas in mammals to the existence of adaptive immunity in most vertebrates.

I don’t see them as parasites. I rather see them as living in symbiosis with the host.
—Marie Mirouze, French National Research Institute for Sustainable Development

But domestication is just one way TEs can drive evolution. Increasingly, scientists are uncovering examples of “wild” TEs—ones that remain autonomous and move about if not actively repressed by the cell—that influence the biology of their hosts in intriguing ways. “So many studies these days [are] pointing to transposons as the answer,” says Edward Chuong, a genomicist with the BioFrontiers Institute at the University of Colorado Boulder. Almost no matter what genetic question is asked, he adds, TEs “tend to be there in the end.”

Chuong points out that TE-derived mutations likely play a significant role in evolution because of their selfish nature: to replicate, transposons need to “convince” the cell’s machinery to help, so their sequences contain lots of elements that can recruit transcription factors and otherwise regulate gene expression. That means that every time a TE moves, it carries regulatory motifs with it that can immediately begin influencing the expression of nearby genes, with potential functional outcomes that influence the overall fitness of the organism.

“If a gene were to evolve a new regulatory element simply by base pair changes, that would presumably take a lot of steps,” Chuong says. But with TEs, “in a single event . . . a gene could acquire a whole new regulatory element.” And that’s just if the element lands near a gene. If it lands within one, it can directly add to the code of exons, or alter intron motifs associated with splicing, or otherwise impact the gene itself. (See illustration.) Plus, TEs don’t always jump alone: sometimes they sweep up sections of nearby code as they leap, which can create duplicates of whole genes or other functional sequences.

According to Chuong and others, TEs’ outsized potential both to affect expression and to alter the genetic code make them important players in evolution, alongside other forms of mutation that are major sources of genetic diversity—the raw material of natural selection. While TEs can sometimes be detrimental, “in the long term they can also be beneficial, and the host can get some advantage [from] the presence of transposable elements,” Mirouze says. With more and more examples now coming out, she adds, it’s becoming clear that TEs are “an engine for evolution.”

VARIABLE ELEMENTS

“You can find transposable elements in virtually all the organisms that have been studied [genetically], from bacteria to eukaryotes,” notes evolutionary biologist Josefa González of the Spanish Research Council (CSIC). But while TEs are nearly universal throughout living organisms, their prevalence varies widely. In some organisms, TEs dominate, accounting for up to 90 percent of the genome, while in others, transposable elements make up only a fraction of the entire genetic code. When abundant, TEs can grow the size of the genome to enormous, unwieldy proportions that continue to baffle scientists.

Data from: PLOS Genet, 17:e1009768, 2021; Plant Physiol, 139:1612–24, 2005; Genome Biol Evol, 5:1886–901, 2013; Genome Biol, 10:107, 2009; Nature, 590:284–89, 2021; Science, 297:1301–10, 2002; Cytogenet Genome Res, 147:217–39, 2015; bioRxiv, doi:10.1101/2021.07.12.451456, 2021; Nature, 420:520–62, 2002; F1000Res, 9:775, 2020; Mobile DNA, 11:23, 2020; PLOS ONE, 6:e16526, 2011; C. elegans II. 2nd edition, CSHL Press, 1997; BMC Bioinformat, 20:484, 2019; PLOS ONE, 7:e50978, 2012; Curr Microbiol, 62:198–208, 2011; J Bacteriol, 194:4124, 2012

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From useful to junk and back again

The notion that TEs are vital to genomes, and not parasites or trash, harks back to the 1950s and Barbara McClintock, who won a Nobel Prize in 1983 for the discovery of transposons in maize: she proposed that TEs play an important role in gene expression in the very first paper on them. But the idea that genetic elements could be mobile clashed with the prevailing view of an organism’s genome as fixed. It would be decades before transposons were described from other organisms and their near-universal presence in genomes became clear. By then, researchers had figured out that these bits of DNA coopt a cell’s machinery, and the parasite framing emerged. Further, research showing that TEs don’t code for essential cellular proteins meant that, at best, they got lumped in with other kinds of noncoding DNA as genetic junk.

Of course, lots of noncoding DNA has come out of the “junk” drawer as genomicists have come to realize its various roles in promoting or suppressing gene expression, for example. But until very recently, TEs have broadly been considered bad for the genome, and pockets of both the popular press and the scientific literature continue to portray them that way. This is in part because transposons remain somewhat mysterious; the sequencing tools that allowed genomics to blossom simply aren’t great for sequencing and mapping transposons, says Chuong. High-throughput methods involve sequencing genomic segments of only a few hundred base pairs at most—too short to accurately annotate TEs due to their repetitive nature, both within their own sequence and in terms of the many full copies that can exist in each genome. For these reasons, many reference genomes are actually incomplete when it comes to mapping their TEs: even the human genome wasn’t completed until 2021.

But with long-read sequencing methods enabling scientists to document the transposon content—the “mobilome”—of individual organisms, TEs are entering the spotlight. And, it turns out, they can and do regulate genes. McClintock was right.

In addition to examples such as the peppered moths, work on fruit flies has demonstrated that TEs can be responsible for remarkable adaptations. Josefa González , an evolutionary biologist with the Spanish Research Council (CSIC) who focuses on the genomics of adaptation, has spent much of her career examining the roles that TEs play in the genomes of Drosophila. Overall, she says, the evidence is clear that TEs have been “an integral part of the genome from the very beginning of evolution.”

TIPs

When scientists want to probe the genetic basis of adaptation, they usually turn to single nucleotide polymorphisms (SNPs). These exist in transposons, but these mobile genetic elements also vary in their location. Transposable element insertion polymorphisms (TIPs) are chunks of chromosome where transposons have inserted in some individuals but not others, and these can be quite common. A 2019 study of 3,000 rice (Oryza sativa) varieties revealed 50,000 TIPs in their genomes, for example.

In flies specifically, TEs are emerging as key regulators of Drosophila gene expression. Last year, González and her colleagues published work showing that TEs inserted in proximity to immune genes have a marked influence on the expression of those genes, even though their insertion occurred relatively recently in the flies’ evolutionary history. And in at least one case—a 1-kilobase TE that inserted itself just upstream of a gene called Bin1—that expression change affects flies’ ability to survive bacterial infection: when the team knocked out the TE with CRISPR, the flies succumbed more readily to Pseudomonas infection, a fate similar to that of flies that never had the TE in that genomic location.

To look for such variations, known as transposable element insertion polymorphisms (TIPs)—places where transposons had inserted in some genomes, but not others—Mirouze and her colleagues developed special software called TRACKPOSON. They have used the program to scan the genomes of 3,000 rice (Oryza sativa) varieties and discovered a staggering 50,000 TIPs, most of which appeared in only one or two of the thousands of varieties of the staple crop plant tested.

It was a wealth of unseen variation to uncover in one of the best-studied plant species, says Mirouze. “This tells you that there’s a lot of diversity that is difficult to capture if you don’t specifically look for it.”

Another surprising example of TE-based diversity, notes Ludwig-Maximilians-Universität München geneticist Arne Weiberg, exists in the mold Botrytis cinerea. According to research by Weiberg and his colleagues, this fungus has weaponized its TEs in the arms race against its plant hosts, allowing it to infect more than 1,400 different plant species.

Weiberg says that the fungus’s generalist strategy intrigued him. Researchers learned back in 2013 that when B. cinerea invades a new host, it releases small RNAs that alter plant gene expression. “They basically fit perfectly into the [RNA interference] pathways that the plant has on board,” he says. The evolution of such RNAs, dubbed virulence factors, through a coevolutionary arms race would seem straightforward in a host-specific plant, but how B. cinerea was so wildly successful across plant species wasn’t immediately obvious to Weiberg.

Work from other researchers had shown that the fungus eases up on transposon silencing during infection, and that this “waking up” of sleeping transposons results in increased expression of virulence factors. But when Weiberg and his colleagues looked more closely, they discovered that influencing expression wasn’t all the transposons were doing: some of them were actually coding for those plant-manipulating RNAs directly, and these RNAs play a pivotal role in pathogenicity, according to results the researchers published last August. Not only do more-pathogenic strains have more TE-derived RNAs, but when Weiberg’s team added TEs to less-pathogenic individuals, those molds became more virulent, causing larger lesions on the leaves of plants they infected.

While more research is needed, Weiberg says TEs could explain the fungus’s promiscuity. The constant duplication and subsequent mutation of TEs could give the mold “such a diverse pool of small RNAs that no matter what plant species it is infecting, there must be at least a few small RNAs that fit to the transcriptome, or the mRNA, of this host species.”

EVOLUTIONARY LEAPS

There are numerous ways that mobile genetic elements can affect evolution. For example, many transposable elements (TEs), often called transposons, contain genes that code for their jumping or copying machinery, and over time these may be “domesticated” through mutation and selection, becoming integral parts of the organisms’ genome. The RAG1 and RAG2 enzymes that mix up DNA segments in immune proteins (antibodies and T cell receptors) are a notable example. “Wild” TEs can also have adaptive potential, creating genetic diversity as they leap. If TEs land inside a gene, they can directly alter coding regions, mRNA splice sites, or expression-related motifs (left). And because transposons often contain transcription factor binding sites and other regulatory sequences, they can alter a gene’s expression even if they land nearby (right). The transposable elements can also alter the genome in other ways—such as by picking up huge chunks of DNA as they jump (not pictured)—that scientists suspect are similarly altering the course of evolution.

Inserting into Genes

Arguably the most immediate and dramatic impacts TEs have on genomes occur when they insert into active genes. They can jump into coding regions, altering protein sequences, or they can insert into noncoding regions and alter gene splicing or expression. This is what happened in peppered moths, when a 22-kb TE inserted into the cortex gene and led to overproduction of melanin, turning dark the normally lightly bespeckled moths and improving their survival in polluted environments.

Inserting near Genes

Unlike point mutations, someTEs come preloaded with genetic motifs that may affect the expression of nearby genes. Certain populations of Drosophila carry the TE insertion FBti0019386, for example, which contains transcription factor binding sites that are activated during a bacterial infection and that increase expression of the immune-related gene Bin1. Flies carrying FBti0019386 are more likely to survive inoculation with a pathogenic strain of Pseudomonas.

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TE mutations: Harder, better, faster, stronger

In addition to a growing body of evidence that transposons can generate diversity in host genomes to drive change over millions of years, Mirouze says TEs are likely major drivers of rapid evolution—changes measured in terms of generations rather than millennia.

While González’s group has yet to conclusively demonstrate that a TE is responsible for rapid evolutionary change in wild flies, some of their analyses have suggested that recent, expression-altering insertions influence the flies’ stress responses, and likely behavior and development as well, she notes. Lab studies suggest that mobile elements account for half or more of all phenotype-altering mutations in the flies. And in wild populations, TIPs are common and some are associated with environmental variables such as temperature and rainfall—exactly what you’d expect if they’re driving adaptation.

I think we’re going to see more and more cases where TEs help explain cases of rapid adaptive changes.
—Lukas Schrader, University of Münster

Another line of evidence for this idea is the fact that many TEs are activated by stress, perhaps serving as a Hail Mary pass for adaptive mutations. Mirouze points to a 2019 study in yeast as an example: when yeast cells were subjected to a novel stressor, the cellular mechanisms that silence transposon activity became less active and TEs began to move, generating genetic variation that accelerated the evolution of resistance to the stressor. Similarly, experiments from a few years earlier point to bacteria’s use of TEs to adapt to acute stress.

Chuong, who says his group’s unpublished work in cattle has suggested that TEs can be activated by immune responses after eons of being silenced, says it’s plausible that TEs are a “major source of variation . . . that could be selected upon” during times of extreme stress, especially when that stress is novel and sudden, such as infection with a deadly pathogen. In such cases, he says, “I think transposons and their activity are much more likely to provide an outsized source of variation compared to littler mutations.”

Other circumstantial evidence for rapid, TE-driven adaptation is found in mosquitoes. In the last 60 years or so, Anopheles coluzzii mosquitoes have become the scourge of sub-Saharan Africa and primary vectors of malaria. One of the reasons for this is that the insect species adapts well to urban environments—something entomologists hadn’t expected, because their close relatives, A. gambiae, are highly susceptible to pollutants and pesticides that are generally more abundant in densely populated areas. It turns out that urban A. coluzzii mosquitoes may have specific TE insertions near genes involved in insecticide resistance and immunity more generally, according to a preprint posted by González and colleagues last April. [Editor’s note: This study has since been published in Genome Research.] Similar insertions have been linked to pesticide tolerance in other mosquito species, so while the findings haven’t been subjected to formal peer review and are “very preliminary,” says González, they point to TEs as the driver of the mosquitoes’ ecological flexibility.

Lukas Schrader, an evolutionary biologist at the University of Münster in Germany, meanwhile, has been investigating the role of TEs in invasive species. Similarly to populations responding to a novel pathogen or other stressor, species entering new environments may need to evolve quickly to survive. When the researchers examined the genomes of the heart node ant Cardiocondyla obscurior, their TEs immediately stood out. There were 34 areas “where over seventy percent of the genomic region is just encoded by transposable elements,” Schrader explains. In the rest of the genome, TEs account for less than 1 percent. Comparing the ant species’ two lineages, one of which is found only in Latin America while the other is found around the globe, the team discovered that while the less invasive ants didn’t lack these “TE islands,” those of the global ant lineage appeared to be more active, suggesting transposons’ confinement to certain regions that might help the species be particularly good at invading novel habitats, he says. The majority of the ant’s genome “is highly conserved, and encodes the basic necessities for being an ant, and then [they] have the super quickly evolving part that’s more specific towards being an invader.”

Ultimately, Schrader says, although TEs are genomic parasites in the strictest sense, they’re not all bad. “I think we’re going to see more and more cases where TEs help explain cases of rapid adaptive changes.”

THE CURIOUS CASE OF SEA SNAKES

When University of Adelaide computational biologist David Adelson and his colleagues set out to annotate the TEs in the genome of the olive sea snake (Aipysurus laevis), they had no idea how strange the animals’ transposons would turn out to be. In addition to finding TEs known from other reptiles, the team discovered seven novel subfamilies of transposable elements, many of which appeared to have been horizontally transferred from unrelated sea creatures. Intrigued, they investigated the TEs in another group of marine serpent called sea kraits (Laticauda spp.) and again found a previously unknown kind of transposon, this time apparently from sea urchins.

What was especially intriguing about that TE, which the team dubbed Harbinger-Snek, is that it underwent massive expansion in the kraits. Now, some 30 million years after it jumped into the animals—perhaps ferried by a parasite or virus—Harbinger-Snek elements account for up to 12 percent of the krait genetic code. And the thousands of copies peppered throughout the genome have landed in some intriguing locations, including potential regulatory regions and introns, which, although noncoding, can influence how the cell’s machinery behaves when transcribing a gene. “There’s enormous potential for these things to have affected gene expression,” Adelson says, and therefore, to have altered the animals’ physiology or behavior.

A small number of the insertions even appeared to overlap directly with coding regions in proposed genes, providing a more direct path to functional change. While Adelson cautions that the annotations aren’t robust—one cannot say for sure, yet, that every section currently marked as a coding region actually is one—it’s certainly possible that at least some of the transposon insertions altered proteins.

Further research suggests that these species weren’t unique. In a preprint posted by Adelson’s team last summer, the researchers claim that all sea-dwelling snakes have transposons obtained from other marine organisms. In fact, the genomes of all of the Australian snakes Adelson and his collaborators examined had such marine TEs, though the ones in terrestrial species appeared to be much more degraded, suggesting they were a lot older than the ones only seen in the aquatic snakes. [Editor’s note: This study has since been published in Genes.]

Adelson says these TEs may help tell the evolutionary story of the sea snakes. Researchers have long thought that Australia’s snake biodiversity stemmed from a small number of terrestrial snakes that rafted their way to the continent. But the presence of ancient marine TEs suggests the colonizing ancestors were at least semi-aquatic—they were spending enough time in the water to pick up aquatic species’ transposons. After the snakes moved onto the Australian mainland, they appear to have acquired a transposon from a lizard. Millions of years later, the fully marine sea snakes and the semi-aquatic sea kraits returned to the water, each gathering new marine TEs in the process.

The data are very preliminary, with population-level studies needed to determine whether TE insertions were advantageous, Adelson says. But he hypothesizes that, given transposons’ habit of rapidly and dramatically altering the genome, the TEs in Australian snakes could have directly aided the animals’ evolutionary journey—to the sea in the first place, then from the sea to the land, and especially back to the sea again. Every time a new transposon entered the genome, he says, it may have provided a burst of genetic diversity, including potentially adaptive changes. And if TE insertions that initially aided aquatic living were neutral once the animals slid back onto land, they could have stuck around for millions of years of terrestrial life, essentially preadapting the snakes to return to the water.

“Perhaps because they had retained some of those amphibious adaptations . . . [they] could make the transition back to aquatic,” he muses. “And that’s interesting, because it means that if we’re going to start looking for adaptations in a very recent timeframe for these events, maybe there are some, but maybe we should be looking at the older ones.”

Correction (January 31): An earlier version of this article had incorrectly referred to Josefa González Pérez as a genomicist for Pompeu Fabra University. She does not use her last name professionally, and is actually an evolutionary biologist with the Spanish Research Council, The Scientist regrets the errors.