Although CRISPR ushered in a golden age of genetic research, there are hundreds of similar systems in nature that hold untapped potential for gene editing. Scientists have now made significant progress in explaining how a mysterious system called SPARDA works.
The CRISPR system allows scientists to edit genetic information more easily than ever before. Although CRISPR is best known for its use in gene editing, it is actually a bacterial immune defense system that has been repurposed for human use.
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molecular argonauts
Mindaugas Zaremba, a co-author of the study and a biochemist at Vilnius University in Lithuania, told Live Science that the researchers had only conducted limited research on the SPARDA system before the new study. They established that the proteins that make up the system employ a kamikaze-like approach to cellular defense, protecting widespread bacterial populations from foreign DNA such as airborne DNA called plasmids and viruses called phages.
“The SPARDA system has been demonstrated to protect bacteria from plasmids and phages by degrading the DNA of both the infected cell and the invader, thereby killing the host cell while preventing further spread of infection within the bacterial population,” Zaremba said.
How SPARDA worked at the molecular level remained unclear, so Zaremba and his team decided to take a closer look at SPARDA’s setup using the AI protein analysis tool AlphaFold, among a suite of other analytical techniques. AlphaFold uses machine learning to predict the 3D shape of proteins based on the arrangement of their underlying building blocks.
The SPARDA system is built from the Argonaute protein, named for its resemblance to the Argonauta octopus. The proteins were originally identified in plants, and seedlings affected by mutations in these proteins developed thin leaves that reminded scientists of the tentacles of an octopus. These argonaute proteins are evolutionarily conserved and present in cells of all three kingdoms of life.
Zaremba’s analysis focused on randomly selected SPARDA systems from two different bacteria. The first, Xantobacter autotrophicus, is a soil-dwelling microorganism that shelters from sunlight and makes food from locally available nitrogen. The second, Enhydrobacter aerosax, was first discovered in Michigan’s Wintergreen Lake and has a built-in airbag that helps it stay afloat in watery environments.
Zaremba’s team excised the SPARDA system from these bacteria and placed it inside E. coli, a reliable model organism, for research. Molecular analysis revealed that each of these Argonaute proteins contains important “activation regions.” They called this area Beta Relay. This is because it resembled a switch in an electrical relay that controlled a machine by switching between an “on” or “off” state.
When the SPARDA system detected an external threat, these switches changed shape. The new shape allowed the protein to form complexes with other activated Argonaute proteins. When that happens, the proteins line up like soldiers on a parade, forming long helical chains. These strands shred all the DNA around them in an extreme reaction that shows no mercy to either the host or the invader. This prevents the infection from spreading to other cells.
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Zaremba’s team then used AlphaFold to scan for beta relays in similar bacterial proteins. The repeated appearance of the same switch suggests that relays are a universal feature of this type of protein.
SPARDA in diagnosis
SPARDA is essential for bacterial defense, but Zaremba’s team argues that the system could also be useful for humans.
Activation of SPARDA is a last resort for bacterial cells and is used only when infection is definitive. Therefore, this system incorporates an incredibly accurate recognition system to detect foreign DNA that requires self-destruction.
Researchers could reuse the system for diagnostic purposes, Zaremba suggested. In that scenario, the beta relay could be modified to only activate if the gene sequence of interest is identified, so it would only respond to the genetic material of the influenza virus or SARS-CoV-2, for example. This mechanism is the basis of existing CRISPR-based diagnostic tools.
However, CRISPR diagnostics is currently limited in its ability to recognize targets only if they are flanked by specific DNA sequences called PAM sequences. These sequences are like protrusions on the end of a plug. If it does not match the socket, the system will not receive power. This means that choosing the right CRISPR protein to match a specific target is essential.
“We already know that SPARDA systems do not require PAM sequences,” Zaremba says. This means that they can act like universal adapters, giving flexibility to future DNA diagnostics and ultimately improving the detection of a variety of bacteria.
CRISPR research won a Nobel Prize and changed science forever. Although the SPARDA work is in the very early stages of research, its inner workings suggest that designing tiny organisms could hold lessons for some of science’s biggest questions.
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