Transposons are critical drivers of bacterial evolution that have been studied for many decades and have been the subject of Nobel Prize winning research. Now, researchers from Cornell University have uncovered mechanisms by which these mobile genetic elements integrate into the chromosomes of bacteria with linear genomes.
Their findings, published in Science in a paper titled, “Telomeric transposons are pervasive in linear bacterial genomes,“ reveal that transposons can target and insert themselves into chromosome ends, or telomeres, a strategy that influences genome stability and bacterial adaptation.
“Bacteria are like these little tinkerers,” noted Joseph Peters, PhD, professor of microbiology at Cornell University. “They’re always collecting these mobile DNA pieces, and they’re making new functions all the time—everything in antibiotic resistance is really about mobile genetic elements and almost always transposons that can move between bacteria.”
Bacterial telomeres
While most bacterial DNA is in the form of plasmids, there are some that have linear DNA that contain telomeres. Though the presence of telomeres at the ends of the linear DNA is similar to eukaryotes, the structure and maintenance of these DNA ends are unique. This study utilized two different types of bacteria, each representing a different type of telomere: hairpin-shaped telomeres or telomeres with a terminal protein.
Cyanobacteria transposons have hairpin-shaped telomers, which, as Peters puts it, “solves the replication problem” of a double-end break, allowing the polymerase to wrap around the end of the DNA during replication. This prevents the need for telomerase to maintain the length of the telomere.
He continued that the second telomeric transposon mechanism is found in Streptomyces, which has aided in the development of many antibiotics. Their telomeres “have an end binding protein that binds to the end, so that makes it not look like a double-strand break, and it itself is able to recruit or make its own primer and recruit a polymerase to solve the end replication problem.”
“In each one of these cases, whether it’s a hairpin or these end binding, they have cis-acting sequences that that system recognizes,” Peters concluded. “So, it’s independent to each individual telomere.”
Tracking transposons in telomeres
The research group focuses on how pieces of DNA move around. Their exploration of transposon movement into telomeres was realized by data mining transposon sequences in relation to telomere sequences in Genbank. Leveraging advanced sequencing technologies, the researchers identified several families of transposons in cyanobacteria and Streptomyces.
Typically, transposons have protein-binding sequences on either end. However, the researchers found that these telomeric transposons have single-sided binding sequences and replace the bacterium’s own telomere. This effectively allows the transposon to function as the telomere, making it an essential component of the bacterial genome.
The team is the first to document these telomeric transposons in bacteria. Peters explained that transposons are insidious, utilizing the telomeres as a safety net for the bacterium to not remove the transposon. “It’s the ultimate parasite because the cell can’t get rid of the transposon because it controls the end. If it killed the transposon, it would lose the telomere, and it would die,” he told GEN.
Modern tech to study ancient systems
Advancements in artificial intelligence (AI) and bioinformatics have played a key role in the team’s discoveries. Peters’ team is excited about the progress in computational tools available for researchers. “We absolutely use AlphaFold all the way,” Peters said about the AI system.
Additional new computational tools have revolutionized genomic analyses. Peters described how his team has used programs including BLAST searches and HHpred because, compared with humans (and with other programs over time), their algorithms are “much, much better at finding matches, even when there’s almost no amino acid sequence, because somehow it’s able to predict something.”
As technology advances, DNA synthesis accessibility has become a game-changer in the field. In the not-so-distant past, the process of creating novel sequences and inserting them into plasmids was technically and financially challenging.
“Another huge thing that I think isn’t really said enough is this idea of DNA synthesis has really been coming down in price,” Peters explained. “Now you can go to one of these biotech companies, and you can get it made and it’s already in plasmids!”
This, he noted, makes the process of moving from hypothesis building to experimentation much faster.
From bacterial immunity to human health
Beyond an advance in understanding evolution, these findings could have practical applications in biotechnology and medicine. The study uncovered a subfamily of telomere-targeting transposons that had utilized a CRISPR system. While CRISPR is typically utilized in bacteria to fight off viral attacks, this subfamily of transposons uses CRISPR to target and integrate into chromosome ends, further supporting prior research from Peters’ lab.
“These transposons captured CRISPR-Cas systems to be able to use them as ways to identify and self-program to sites they really want to go into,” Peters told GEN. “It was this totally ingenious way that they evolved on their own.”
As interest in harnessing transposon systems for gene-editing applications grows, researchers recognize both the promise and the challenges ahead. “It’s a good inspiration for ideas.” However, he added that it doesn’t solve all of the problems. Nor can it be put into humans to cure everything.
He described how gene editing comes in three groups: base editing, prime editing, and large-program gene delivery. Transposons, he said, are a good inspiration for the third group: “These elements are just really ready for that.”
Looking ahead, he hopes to apply transposon-based systems to gene editing. Peters explained that many genetic diseases have single nucleotide errors in the DNA sequence. Based on the current path to creating disease treatments, each individual genetic change through base or prime editing would require a unique set of trials. Instead, Peters emphasizes that broadening the scope of genetic replacement would be a better and more streamlined solution. “You really want to replace that exon, because then you can cure a hundred diseases at one time.”
However, delivery systems remain a key challenge. “To really meet the potential for all these, you really need some kind of delivery [mechanism] that can allow this cargo range,” Peters noted. “I think it is safe to say that a lot of these things are aspirational, and that we are going to make a great machine that we don’t know how to deliver yet.”
Despite these hurdles, Peters remains optimistic. “That’s still a challenge. There’s a lot of money and a lot of companies going into that. So, I think that is something that will be solved.”