A ‘crazy’ discovery in bacteria raises fundamental questions about the composition of our own genome – and reveals a potential source of material for new genetic therapies.
Since the genetic code was first deciphered in the 1960s, our genes have seemed like an open book. By reading and decoding our chromosomes as linear strings of letters, like sentences in a novel, we can identify the genes in our genome and learn why changes in a gene’s code affect health.
This linear rule of life was thought to govern all life forms – from humans to bacteria.
But a new study from Columbia researchers shows that bacteria break that rule and can create free-floating and short-lived genes, raising the possibility that similar genes exist outside our own genome.
“What this discovery undermines is the idea that the chromosome has the full set of instructions that cells use to produce proteins,” said Samuel Sternberg, associate professor of biochemistry and molecular biology at Vagelos College of Physicians and Surgeons, who led the study with Stephen Tang, an MD/PhD student at the medical school.
“We now know that, at least in bacteria, there may be other instructions that are not preserved in the genome and are still essential for the cell’s survival.”
“Amazing” and “alien biology”
The scientific response had already made headlines a few months ago when the article first appeared as a preprint. In a Nature News article, scientists called the discovery “alien biology,” “astonishing” and “shocking.”
“It repeatedly left us in disbelief,” says Tang, “and we went from doubt to amazement as the mechanism gradually came into view.”
Bacteria and their viruses have been at war for centuries, as viruses try to inject their DNA into the bacterial genome and bacteria devise cunning methods (e.g. CRISPR) to defend themselves. Many bacterial defense mechanisms remain unexplored but could lead to new tools for genome editing.
The bacterial defense system that Sternberg and Tang chose to investigate is strange: the system involves a piece of RNA with an unknown function and a reverse transcriptase, an enzyme that synthesizes DNA from an RNA template. The most common defense systems in bacteria cut or break down incoming viral DNA, “so we were amazed at the idea of defending the genome through DNA synthesis,” says Tang.
Free-floating genes
To learn how this strange defense works, Tang first created a new technique to identify the DNA produced by the reverse transcriptase. The DNA he found was long but repetitive and contained multiple copies of a short sequence within the immune system’s RNA molecule.
He then realized that this part of the RNA molecule folds into a loop, and the reverse transcriptase travels around the loop numerous times to create the repetitive DNA. “It’s like you were planning to copy a book, but the copier started printing the same page over and over again,” says Sternberg.
The researchers originally thought that perhaps there was something wrong with their experiments, or that the enzyme made a mistake and the DNA it created was useless.
“That’s when Stephen did some ingenious research and discovered that the DNA molecule is a fully functioning, free-floating, transient gene,” says Sternberg.
The protein encoded by this gene, the researchers discovered, is a crucial part of the bacteria’s antiviral defense system. Viral infection causes the production of the protein (named Neo by the researchers), which prevents the virus from replicating and infecting neighboring cells.
Extrachromosomal genes in humans?
If similar genes were floating free in cells of higher organisms, “that would really be a groundbreaking discovery,” says Sternberg. “There may be genes or DNA sequences that are not found in any of the 23 human chromosomes. Perhaps they are only made in certain environments, in certain developmental or genetic contexts, and yet provide critical coding information that we rely on.” for our normal physiology.”
The lab is now using Tang’s methods to search for human extrachromosomal genes produced by reverse transcriptases.
Thousands of reverse transcriptase genes exist in the human genome, many of which have yet undiscovered functions. “There is a significant gap that needs to be filled and that could reveal more interesting biology,” says Sternberg.
Source of gene editing
Although gene therapies that take advantage of CRISPR editing are in clinical trials (and one was approved last year for sickle cell disease), CRISPR is not the perfect technology.
New techniques that combine CRISPR with a reverse transcriptase give genome engineers more power. “The reverse transcriptase gives you the ability to write new information at sites that CRISPR removes, which CRISPR alone can’t do,” says Tang, “but everyone is using the same reverse transcriptase that was discovered decades ago.”
The reverse transcriptase that Neo creates has certain properties that may make it a better option for genome editing in the laboratory and for creating new gene therapies. And even more mysterious reverse transcriptases exist in bacteria waiting to be discovered.
“We think bacteria may have a wealth of reverse transcriptases that could be a suitable starting point for new technologies once we understand how they work,” says Sternberg.
