Dana-Farber researchers have discovered ancient bacterial defenses and anti-defenses that may persist in some form in humans today and could provide insights into new approaches to cancer research and treatment.
The tripwire is a go-to booby trap in movies. An aggressor trips over an unseen wire, setting off a trap that foils their plans. It’s an oldie — and according to new Dana-Farber Cancer Institute research, it is much, much older than moving pictures.
Bacteria have a deep defensive playbook that has evolved over millennia as the organisms have learned to defend themselves against increasingly cunning invaders. That playbook contains DNA that codes for a molecular tripwire that defends against bacterial viruses called phages, according to a study from the lab of Philip Kranzusch, PhD, of the Department of Cancer Immunology and Virology. This molecular tripwire evolved eons ago and could potentially be playing a role in human immunity today.
Similarly, another study from the Kranzusch lab and collaborators identified a molecular sponge created by phages to absorb bacterial defense signals and thwart calls for aid. This study also shows that the molecular “alphabet” bacteria use to generate calls for aid is far more complex than previously understood.
“Our lab studies genes of unknown function, and we’re interested in bacterial immune systems,” says Kranzusch. “We are trying to understand how the immune system is controlled so that, in the future, that information can help inform the design of better therapeutics that leverage the immune system to fight cancer.”
The Hailong system’s unexpected tripwire mechanism
A molecular trip wire. Courtesy of Joel Tan.
When Joel Tan joined the Kranzusch lab as a graduate student, Kranzusch pointed him to an interesting pair of genes of unknown function that were part of a cluster of defense-related genes in bacterial genomes. One of the genes looked like it encoded for an enzyme called a nucleotide transferase (NTase), a type of enzyme the lab has studied before. It was right in the lab’s wheelhouse, and Kranzusch thought it might be a straightforward project for Tan.
“Famous last words,” says Kranzusch. “I thought it would be similar to what we’ve seen before, but of course everything was different.”
The first big difference became evident when Tan determined the molecular structure of the NTase. He’d been running some tests on the enzyme that hadn’t been working as expected and the structure explained why. The NTase appeared to be organized to continually create a signal, a long single-stranded thread of DNA. Other NTases the team is familiar with are organized to create a signal only when a threat is detected.
The second surprise came when Tan tried to study the second gene of interest. When he tried to have a cell produce it without the NTase, the cells did not survive. The team realized, with help from collaborators at Harvard University, that the two genes together set up a tripwire.
Tan named the two-gene system Hailong, after a Chinese ocean god of protection, and the two genes HalA and HalB (the NTase). The HalB protein produces the single-stranded DNA. That signal tells HalA, a membrane protein, to keep an ion channel domain closed.
A molecular sponge. Courtesy of Renee Chang.
“This system is always running,” says Tan. “But if a virus disrupts that perpetual process, that trips the wire and tells the immune system it is time to respond.”
When tripped, HalA opens the channel domain, which puts the cell into stasis. The cell’s metabolism is shut down and all activities halt, including the replication of the viral invader.
An extended alphabet for immune signals and the molecular sponge
Immune defenses like Hailong have evolved over millennia through an evolutionary battle between bacteria and phage. Some phages will trip the wire. Others — and there are predicted to be over 10 to the power of 31 unique phages — do not.
“There’s evolutionary pressure for the bacteria to develop ways to defend against threats in the environment,” says Renee Chang, who is also a graduate student in the Kranzusch lab and who is one of three first-authors on another Nature paper related to bacterial immunity.
Chang and collaborators at Vilnius University in Lithuania and the Weizmann Institute of Science in Israel studied the TIR protein domain, which gives proteins the ability to recognize patterns and identify pathogens. TIR domains are found in bacteria, plants, and animals, including humans.
Specifically, they studied the TIR protein in a bacterial defense system called type II Thoeris, which sends a signal when an invader is recognized.
The team found that the TIR protein in the system creates a signal using a more diverse set of building blocks than ever seen before. The signal is comprised of the building blocks of DNA, which are molecules called nucleotides, and proteins, which are amino acids. The mixture expands the realm of possible signals, the same way adding numbers to a letter-based password makes the number of possible passwords larger and makes individual passwords harder to guess.
“The permutation space grows exponentially, so the types of signals likely to exist in nature are much more diverse than we would have imagined,” says Kranzusch. “This is the first time we’ve seen them combined to synthesize an immune signal.”
The paper also details how phage counterattack by creating a structure that recognizes, captures, and sequesters those signals, like a sponge. The signals are trapped, so the defense system doesn’t receive them.
How ancient bacterial defenses are relevant to human cancer
Tan is investigating potential Hailong-like proteins in the human genome to learn more about their role in controlling responses to cancer in human cells. Chang is interested in the molecular sponges produced by phage and is exploring their potential use as tools to search for novel types of immune signals.
“We’re pushing our understanding of immune processes in new directions and considering how immune signals are being used for different functions than we’d thought about before,” says Kranzusch. “These discoveries could someday lead to new insights that advance our understanding of cancer immunity and enable new approaches the cancer therapy.”
Written by: Beth Dougherty