A ‘loopy’ discovery in bacteria is raising fundamental questions about the makeup of our own genome — and revealing a potential wellspring of material for new genetic therapies.
A “loopy” discovery in bacteria is raising fundamental questions about the makeup of our own genome — and revealing a potential wellspring of material for new genetic therapies.
Ever since scientists decoded the genetic code back in the 1960s, it seemed like our genes revealed their secrets clearly. By interpreting our chromosomes as straight strings of letters, akin to sentences in a book, we can pinpoint genes in our DNA and understand how alterations in a gene’s sequence can impact our health.
This straightforward principle was believed to apply universally, from humans to bacteria.
However, a recent study by researchers at Columbia University has thrown this idea into question, demonstrating that bacteria can generate transient, free-floating genes, which suggests that similar genes might exist beyond our known genome.
“What this finding challenges is the belief that the chromosome contains the entire set of instructions required for cells to create proteins,” explains Samuel Sternberg, an associate professor of biochemistry and molecular biology at the Vagelos College of Physicians and Surgeons, who led the study alongside MD/PhD student Stephen Tang.
“We now understand that, at least in bacteria, there may be additional instructions that are not documented in their genome but are still vital for the survival of the cell.”
“Astonishing” and “alien biology”
The scientific community had already expressed their astonishment a few months ago when the research was first published in its initial form. An article from Nature News described the finding as exhibiting “alien biology,” calling it both “astonishing” and “shocking.”
“It constantly left us in disbelief,” Tang recalls, “and as the mechanism became clearer, we transitioned from skepticism to wonder.”
Bacteria and the viruses that target them have engaged in an ongoing struggle for ages, where viruses attempt to integrate their DNA into the bacterial genome while bacteria innovate methods (like CRISPR) to defend against these attacks. Many bacterial defensive strategies are still undiscovered, which may lead to novel genome editing technologies.
The unique bacterial defense system that Sternberg and Tang focused on is rather peculiar: It utilizes a piece of RNA with an undefined role and a reverse transcriptase enzyme, which constructs DNA from an RNA template. The most typical bacterial defense mechanisms cut or degrade incoming viral DNA, making the concept of defending the genome via DNA synthesis puzzling for Tang.
Free-floating genes
To understand how this unconventional defense operates, Tang developed a novel technique to identify the DNA generated by the reverse transcriptase. The DNA he discovered was lengthy yet repetitive, featuring multiple instances of a brief sequence found within the RNA of the defense system.
He subsequently realized that this segment of the RNA folds into a loop, allowing the reverse transcriptase to spiral around it multiple times, producing the repetitive DNA. “It’s like trying to photocopy a book, but the copier keeps churning out the same page repeatedly,” explains Sternberg.
The researchers initially suspected there was an issue with their experiments or that the enzyme was errantly producing meaningless DNA.
“That’s when Stephen conducted some clever investigations and uncovered that the DNA molecule is a fully functional, free-floating, temporary gene,” Sternberg states.
The protein encoded by this gene, which the researchers dubbed Neo, was found to be a crucial component of the bacteria’s defense against viruses. Viral infections prompt the production of this protein, which inhibits the virus from reproducing and infecting adjacent cells.
Extrachromosomal genes in humans?
If similar free-floating genes are identified within the cells of more complex organisms, Sternberg believes “that would be an absolutely revolutionary finding.” “There could be genes or DNA sequences that are not present in any of the 23 human chromosomes. Perhaps they are only produced under specific conditions, in particular developmental or genetic contexts, yet are essential for our normal biological functions.”
The lab is currently utilizing Tang’s techniques to search for human extrachromosomal genes generated by reverse transcriptases.
Thousands of reverse transcriptase genes are already known within the human genome, many of which have undefined functions. “There exists a considerable void that, if filled, might unveil some fascinating biological insights,” Sternberg notes.
A new source for gene editing
While gene therapies utilizing CRISPR editing technology are in clinical trials (with one receiving approval last year for sickle cell disease), CRISPR isn’t flawless.
New methods that integrate CRISPR with a reverse transcriptase provide genome engineers with enhanced capabilities. “The reverse transcriptase allows the incorporation of new information at sites where CRISPR makes cuts, something CRISPR alone cannot achieve,” Tang explains, “but common practice relies on the same reverse transcriptase that was identified decades ago.”
The reverse transcriptase responsible for Neo possesses specific characteristics that might make it a superior choice for laboratory genome editing and the development of new gene therapies. Moreover, other uncharted reverse transcriptases exist in bacteria and await exploration.
“We believe that bacteria may hold a wealth of reverse transcriptases that could serve as valuable starting points for new technologies, once we grasp their mechanisms,” Sternberg concludes.
